Judiciary officials today took away at least five student leaders who had organised Iran's largest pro-reform protests for more than three years, student and official sources said.
More arrests are likely, said officials in the Islamic Republic.
Analysts said the detentions may revive unrest on university campuses, which had been calmer in recent days after government officials urged students to end their demonstrations.
Students have held two weeks of almost daily class boycotts and rallies of up to 5,000 people to call for freedom of speech and major political reform since a hardline court sentenced reformist academic Hashem Aghajari to death.
Mr Ebrahim Rezai Babadi, deputy governor of Tehran, said the arrests had been carried out by the Revolutionary Courts, a branch of the hardline judiciary that normally deals with public order and national security offences.
The arrests came amid mounting confusion over the fate of Aghajari, a history lecturer whose death sentence for questioning clerical rule sparked the student protests.
Although judiciary officials have said they will comply with an order by Mr Khamenei to review his case, the chief prosecutor said today the court's verdict would stand unless Aghajari appealed within 20 days of being sentenced.