The students were expressing their support for France, which last week, urged the military government not to use "artificial pretexts" to exclude candidates from the promised presidential election.
Witnesses said some of the students were forced to do press-ups and flogged, while dozens were dragged away. Passers-by were also seen being beaten.
The students are mainly supporters of former prime minister Alassane Ouattara, who could be barred from standing in September's scheduled presidential election by a new constitution, which requires all candidates to be born of Ivorian parents.
"We have a petition in support of France's position with 10,000 signatures on it," a protester told Reuters news agency.
Anti-French slogans
A rival group of students briefly occupied the French embassy in Abidjan last Friday, accusing the former colonial power of meddling in the internal affairs of Ivory Coast.
The protests followed remarks made by French Co-operation Minister Charles Josselin that nobody should be excluded from presidential elections, being interpreted in some quarters as support for Mr Ouattara. France has since said Ivory Coast must organise elections that are above reproach. In a statement, the French Foreign Ministry also dismissed the controversy aroused by Mr Josselin's statement as groundless. Mr Ouattara, was prevented from leaving for France last week, despite the lifting of travel restrictions on leaders of political parties. His opponents say he is from neighbouring Burkina Faso. He says he is Ivorian. The row has exposed ethnic tensions in what used to be one of West Africa's most stable countries. Ivory Coast has a population of about 19 million, but about 40% are immigrants - mostly plantation workers from neighbouring states - who cannot vote.