The Salaamnews and Parlemannews sites said the clashes occurred Wednesday in the central city of Isfahan as mourners gathered to honor Grand Ayatollah Hossein Ali Montazeri, who died on Sunday.
The reports said there were numerous injuries and that more than 50 people were arrested, including a pro-opposition cleric.
Parlemannews said hard-line Basij militiamen beat the mourners and used tear gas and pepper spray to disperse people at a local mosque.
The reports could not be independently confirmed.
Montazeri's death has set off large memorial ceremonies that turned into pro-opposition street protests in defiance of a months-long government crackdown.
Videos posted on YouTube and other social networking sites - often used by the Iranian opposition movement - showed what were described as anti-government demonstrations at Isfahan Technical University on Tuesday. The videos' content could not be independently verified.
Tens of thousands of Iranian mourners turned the funeral procession for Montazeri on Monday into an, chanting "death to the dictator" and other slogans in support of the opposition amid heavy security.
Witnesses said security forces clamped down in Iran's holy city of Qom where massive crowds streamed in for the funeral rites for, who died Sunday at age 87.