The Norooz site said attackers insulted Sanei, beat up some of his associates and broke windows. There was no immediate official comment.
The reported incident took place a day after huge crowds turned out in Qom for the funeral of Iran's leading dissident cleric, Grand Ayatollah Hossein Ali Montazeri, and many chanted anti-government slogans, websites said.
Earlier on Tuesday, the semi-official Fars News Agency said pro-government theology students had staged a rally in Qom to protest the insult against sanctities during Montazeri's funeral procession.
The demonstration ended outside Sanei's home, Fars said, but it was not clear whether it was linked to the attack reported by Norooz.
The demonstrators chanted the city of Qom is no city for hypocrites and signed a statement calling for measures toward the defrocking of Yusuf Sanei's religious authority, Fars said.
One of the signatories, cleric Ahmad Panahian, said: The trenches of the hypocrites in Qom must be destroyed.
Sanei said after Iran's disputed presidential election in June, which returned Mahmoud Ahmadinejad to office, that many Iranians were unconvinced about the result because of voting ambiguities and he urged the authorities not to violate people's rights.
MOUSAVI STRIPPED OF ART POST
Separately, the reformist Jaras website quoted Montazeri's son, Ahmad Montazeri, as saying traditional memorial services held on the third and seventh day of mourning for the cleric will not take place due to security considerations.
Another website, Ayande, said after Monday's funeral Montazeri opponents stopped his memorial service in a mosque.
The reports from Qom could not be verified independently because foreign media were banned from reporting directly on protests and were told not to travel to the funeral.
Montazeri, who died during Saturday night aged 87, was an architect of the 1979 revolution that overthrew the U.S.-backed shah and was once named to succeed Ayatollah Ruhollah Khomeini as supreme leader of the Islamic state. But Montazeri fell from grace after criticizing the mass execution of prisoners.
Montazeri was viewed as the spiritual patron of the pro-reform opposition movement that led the big protests that followed the presidential elections.
Ahmadinejad's re-election in a vote that losing opposition candidates said was rigged kindled the biggest unrest in the Islamic Republic's 30-year history and split the political and clerical establishment.
In a move underlining that split, Fars said a government cultural body had voted to strip moderate opposition leader Mirhossein Mousavi, a former prime minister who came second in the election, from the post of directing Iran's Academy of Arts.
Despite scores of arrests and security crackdowns, opposition protests have repeatedly flared up since the vote.
Montazeri's death occurred in the tense run-up to Ashura, a politically important Shi'ite religious commemoration that offers the opposition another opportunity to show its strength.
(Writing by Fredrik Dahl; Editing by Jon Hemming/David Stamp)