Tensions have been running high between the two camps since the revolt in January scrapped a ban on Islamists and paved the way for an Islamic party to come to power at the head of a coalition government.
The latest round of protests was sparked when a group of Islamists occupied a university campus near the capital to demand segregation of sexes in class and the right for women students to wear a full-face veil.
About 3,000 Islamists gathered outside the constituent assembly in the Bardo district of Tunis on Saturday, separated by a police cordon from a counter-protest by about 1,000 secularists.
The Islamists say the secularist elite which has run the country since independence from France is still restricting their freedom to express their faith. Their rivals say the Islamists are trying to impose an Islamic state in what has been one of the Arab world's most liberal countries.
The Islamist protesters at the rally carried placards saying: "We support the legitimacy of the majority!," "Islamic Tunisia is not secular!," and "No to secularist extremism."
An Islamist protester, Nourdine Machfer, said the Tunisian people had expressed their will when they handed victory to the Islamic Ennahda party in an election in October.
"It's bizarre. Today in Tunisia we are living in a dictatorship of the minority," Machfer told Reuters. "They should respect the will of the people, who have made their views known."
Ennahda issued a statement saying that it did not support the Islamist protest outside Parliament.
However, secularist opponents said they believed Ennahda's true agenda was to create an Islamic state by stealth. "The Islamists ... want to use the constitution to take power, and stage a coup d'etat against democracy," said one of the secularist protesters, Raja Dali.
"They want to give all the power to the prime minister," she said, referring to senior Ennahda official Hamadi Jbeli who is his party's nominee to lead the coalition government.
