Peter Beaumont, Patrick Kingsley and Angelique Chrisafis:

A series of repressive dictatorships have been brought down in north Africa, but the ensuing struggles for power have left a vacuum that has allowed the rise of an extremist movement that is gathering both force and supporters

Late last year, largely unnoticed in the west, Tunisia's president, Moncef Marzouki, gave an interview to Chatham House's The World Today. Commenting on a recent attack by Salafists – ultra-conservative Sunnis – on the US embassy in Tunis, he remarked in an unguarded moment: "We didn't realise how dangerous and violent these Salafists could be … They are a tiny minority within a tiny minority. They don't represent society or the state. They cannot be a real danger to society or government, but they can be very harmful to the image of the government."

It appears that Marzouki was wrong. Following the assassination of opposition leader Chokri Belaid last Wednesday – which plunged the country into its biggest crisis since the 2011 Jasmine Revolution – the destabilising threat of violent Islamist extremists has emerged as a pressing and dangerous issue.

Violent Salafists are one of two groups under suspicion for Belaid's murder. The other is the shadowy, so-called neighbourhood protection group known as the Leagues of the Protection of the Revolution, a small contingent that claims to be against remnants of the old regime, but which is accused of using thugs to stir clashes at opposition rallies and trade union gatherings.

The left accuses these groups of affiliation with the ruling moderate Islamist party, Ennahda, and say it has failed to root out the violence. The party denies any link or control to the groups. But it is the rise of Salafist-associated political violence that is causing the most concern in the region. Banned in Tunisia under the 23-year regime of Zine El Abidine Ben Ali, which ruthlessly cracked down on all forms of Islamism, Salafists in Tunisia have become increasingly vocal since the 2011 revolution.

The Salafist component in Tunisia remains a small minority, but it has prompted rows and mistrust among secularists and moderate Islamists. The Salafists are spread between three broad groups: new small political movements that have formed in recent months; non-violent Salafis; and violent Salafists and jihadists who, though small in number, have had a major impact in terms of violent attacks, arson on historic shrines or mausoleums considered to be unorthodox, demonstrations against art events – such as the violence at last summer's Tunis Arts Spring show, which was seen to be profane – and isolated incidents of attacking premises that sell alcohol outside Tunis.

It is not only in Tunisia. In Egypt, Libya and Syria, concern is mounting about the emergence of violent fringe groups whose influence has already been felt out of all proportion to their size.

In Egypt last week, it was revealed that hardline cleric Mahmoud Shaaban had appeared on a religious television channel calling for the deaths of main opposition figures Mohammed ElBaradei – a Nobel peace prize laureate – and former presidential candidate Hamdeen Sabahy.

In Libya in recent months, Salafists and other groups have been implicated in a spate of attacks, including the assault on the US consulate in Benghazi in which two Tunisians were suspected.

Among the countries which succeeded in removing their authoritarian leaders in the Arab spring, Tunisia has faced the greatest challenges in its transition from Salafi-inspired jihadism. These groups – once ruthlessly suppressed by Ben Ali – have re-emerged with a vengeance over the past two years.

In May last year, armed Salafists attacked a police station and bars selling alcohol in the El Kef region. A month later, a trade union office was firebombed. In September, a Salafist mob stormed the US embassy in Tunis and an American school.

If it is difficult to describe what is happening, it is because of terminology.

Although many of those involved in violence and encouraging violence could accurately be called Salafis, they remain an absolute minority of a wider minority movement that has emerged as a small but potent political force across post-revolutionary North Africa.

Although the encouragement to violence from this minority has been most marked in Tunisia, it has not been absent in Egypt.

"We've already started to see real threats," said Shadi Hamid, director of research at the Brookings Doha Centre last week. "There are many instances in Egypt where Salafis have used the language of incitement against opponents."

Last year, one Egyptian Salafi cleric, Wagdi Ghoneim, called for a jihad on protesters against President Mohamed Morsi, a demand he repeated this month. Another – Yasser el-Burhamy – reportedly banned Muslim taxi-drivers from taking Christian priests to church.

Yasser el-Shimy, Egypt analyst for the Crisis Group said: "All it takes is for one guy to take it upon himself to carry out a fatwa. But the prospects of that happening in Egypt are less – or certainly not more – than they are in Tunisia. In Egypt, there was a deeper integration of Salafis into the political process as soon as the revolution had taken place."

Most tellingly, two leading Egyptian Salafis last week condemned the death threats against ElBaradei and Sabbahi.

A spokesman for al-Gama'a al-Islamiyya – which only last week called for the crucifixion of masked Egyptian protesters known as the Black Bloc – "rejected" assassinations as a political tool, while the leader of the Nour party, Egypt's largest Salafi group, went further, criticising "all forms of violence".

Nader Bakkar, a spokesman for the Nour party, said: "The Salafis in Tunisia are not organised well and they don't have the scholars who can teach them how to deal peacefully with things that they don't like in their country. It gives you a clear vision that we will not see in Egypt what we saw happen in Tunisia."

Bakkar also argued that Shaaban, the cleric who issued the fatwa against ElBaradei and Sabbahi, had little currency in Egyptian Salafism.

"He doesn't have many followers," said Bakkar, who claimed that Shabaan came from a school of Salafism that had preached obedience to former dictator Hosni Mubarak, and whose reputation had therefore been ruined in the post-revolution period.

The main Salafist political parties, which are represented in parliament, have far more of a stake in democratic transition than in Tunisia and Libya.

In Libya, Islamist violence, in some cases inspired by Salafism, has followed its own trajectory. After more than a year of violence that came as much from the competition between rival groups who fought former dictator Muammar Gaddafi for power and influence, recent incidents have had a more jidahi flavour even as Salafist groups have attacked Sufi shrines and demanded that women be covered.

If there are differences between the strands of Salafist extremism in North African countries, there are some striking similarities. Like Egypt – as Anne Wolf pointed out in January in a prescient essay on the emerging Salafist problem in Tunisia for West Point's Combating Terrorism Centre, "certain territories … have traditionally been more rebellious and religiously conservative than others. Tunisia's south and interior, in particular, have found it difficult to deal with the modernisation policies launched by the colonial and post-independence governments, whose leaders came from more privileged areas."

And while violence – and the threat of violence – by the "minority of the minority" of Salafis has the potential to disrupt the post-revolutionary governments of the Arab spring, for the new Islamist governments it also poses considerable political problems, which are perhaps as serious.

In Tunisia, the government estimates that 100 to 500 of the 5,000 mosques are controlled by radical clerics. Although the majority of Salafists are committed to non-violence, the movement has been coloured by the acts of those following a jihadi stream.

That has created problems for Ennahda, which secular opponents suspect of secretly planning with Salafis the "re-Islamisation" of Tunisia, not least because of the government's unwillingness or inability to move against the most extreme Salafi groups.

Indeed, when an al-Qaida in the Islamic Maghreb cell was broken up in Tunisia last year, all its members were also found to be active in another Salafist grouping – Ansar al-Sharia, founded by Abou Iyadh. He was jailed for 43 years under ex-dictator Ben Ali's regime after being extradited from Turkey, but was freed under an amnesty for political prisoners following the 2011 revolution that ousted the president.

The jihadist strand has recently been vocal in its condemnation of the intervention by France in its former colony of Mali, which has increased anti-French feeling. Algerian officials said 11 of the 32 Islamist gunmen who overran the In Amenas gas field last month were Tunisian. Tunisian jihadists are said to have left for Syria.

For Ennahda – as a number of analysts pointed out last year – confronting extremist Salafist violence has become a challenging balancing act. Fearful of radicalising the wider movement by cracking down too hard – as the former Ben Ali regime did – it has sought instead to have a dialogue with those renouncing violence by condemning the "rogue elements". This is a policy that has led to accusations that it has been too soft or has secretly tolerated violence against secular opponents such as the murdered Belaid.

As Erik Churchill and Aaron Zelin argued in an article for the Carnegie Endowment for Peace last April, "this position opens the door for secular groups to criticise … the ruling party's actions [as] evidence of a double discourse – conservative in private and moderate in public".

In particular, Tunisia's secular leftist parties were critical of the setting up of a religious affairs ministry under Noureddine al-Khademi, an iman affiliated to the Al-Fateh mosque in Tunis, known for its Salafist presence and protests.

Khademi's office vowed that several hundred mosques in Tunisia which had been taken over by Salafist preachers after the revolution would be brought back under moderate control. Last year, his office said that around 120 remained controlled by extremist preachers, of which 50 were a serious problem.

Even MPs in Ennahda have recently woken up to the problem. Zied Ladhari, an MP for Sousse in the Assembly said the Salafist issue was a concrete part of the heritage of the Ben Ali era and "must be handled in a concrete manner".

He said violent Salafism and jihadism "presents a danger for the stability of the country", while non-violent Salafism – "a way of life and literal reading of Islam" often "imported and foreign to our society"– was something that Ennahda distinguished itself from.

"The violent element must be fought very firmly by police and the law," said Ladhari. "Then there should be dialogue with the peaceful element, in the hope of evolution through dialogue. It's more of a sociological issue than a political one."

He said social-economic issues and fighting poverty and social exclusion were crucial. He said: "We have to deal with it seriously and with courage, a drift must not take hold."

Selma Mabrouk, a doctor and MP who recently quit the centre-left Ettakatol party in protest over the coalition's stance on the constitution and power-sharing, said: "The problem is the violent strain of Salafism, not the strain of thought, because we now have freedom of expression, everyone can have their views."

She warned against an "ambiguous" stance by Islamist party Nahda and the centre-left CPR in the coalition towards street violence, hate speech and attacks which she said were going unchecked. She was also highly critical of the fact that two Salafists arrested for the US embassy attack died in prison after a long hunger strike without a proper trial procedure coming into effect.

She said: "There is this ambivalent attitude from the government, a permissivity on street violence on one side and, on the other hand, indifference to prisoners and the hunger strike."

• This article was amended on 10 February 2013. In the original a paragraph by the writers was wrongly marked as a quote from Shadi Hamid. This has been corrected.

What is salafism?

■ An ultraconservative religious reform movement within Sunni Islam, which has received backing from Saudi Arabia, Salafism calls for a return to the moral practices of the first Muslims.

■ It has incorrectly become synonymous with jihadi ideology, however. Salafists – while extremely puritanical – reject suicide bombing and violence.

■ A minority movement in Islam, it is growing and has become increasingly politically important, not least in Egypt where Salafist parties came second in last year's parliamentary elections to Mohamed Morsi and the Muslim Brotherhood.

- guardian