Violence broke out in the central city of Kairouan and in the capital Tunis.
The government last week said it had barred the Salafist movement Ansar al-Sharia from holding its annual congress in Kairouan, saying it posed a threat to public security.
The group urged its supporters instead to gather for the meeting in the Tunis suburb of Ettadhamen.
Some 500 supporters were reported to have descended on Ettadhamen on Sunday, erecting barricades and hurling stones at police who responded by firing tear gas and shooting into the air.
A massive police presence in Kairouan also failed to prevent Salafists from gathering there. Scuffles broke out in the city centre as police used tear gas to disperse the stone-throwing protesters.
Ansar al-Sharia said its spokesman, Seifeddine Rais, had been arrested but it was not immediately clear why.
The government on Friday said it was banning Ansar al-Sharia from gathering in Kairouan because it had “shown disdain for state institutions, incited violence against them and poses a threat to public security”.
Ansar al-Sharia used its Facebook page to say it was moving its congress to Ettadhamen.
Last year’s congress in Kairouan attracted some 4,000 supporters.
The governing Ennahda party was elected following the overthrow of President Zine el-Abidine Ben Ali in January 2011.
It governs in coalition with two non-religious parties and has promised not to ban alcohol or impose the veil.
But Salafists want stricter Islamic laws imposed in Tunisia, and are demanding the introduction of Sharia.