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The protesters also set fire to a dozen or so motorcycles as well as rubbish bins, another witness said.
Earlier, supporters of Iran's hardline president Mahmoud Ahmadinejad clashed with supporters of defeated presidential candidate Mirhossein Mousavi on the streets of Tehran.
The opposition supporters defied a heavy security presence and dire warnings from regime officials about the consequences of any effort to use the event to mount the protest, the first against Ahmadinejad's hotly disputed June re-election in two months.
One witness, speaking to FRANCE 24's Observers website, reported that tens of thousands of supporters of Mirhossein Mousavi, who lost a disputed presidential election to Ahmadinejad in June clashed with Basij militia, and that police had intervened to keep the two groups apart.
“There were clashes between pro-Mousavi supporters and Ahmadinejad supporters, who were backed up by Basij militiamen," said Amir (not his real name). “But the police got between the two groups. The Basij tried to move the pro-Mousavi supporters back, but the police intervened.
“The attacks and provocation came from the side of the Ahmadinejad supporters. We expect to see further demonstrations in different parts of Tehran by Mousavi supporters today.”
Other witnesses said security forces and clashed with opposition supporters and arrested at least 10 of them during annual anti-Israel rallies in central Tehran on Friday.
"Security forces just arrested over 10 people," a witness told Reuters. "They are pushing protesters and beating them. Supporters of Ahmadinejad are beating supporters of Mousavi near the Vali-ye Asr street (in central Tehran). At least two protesters were injured."
Iran's official IRNA news agency also reported that crowds of angry pro-government marchers assaulted the Mousavi's car, forcing him to leave the rally.
The report said that the opposition leader joined the rally with his bodyguards at about noon (0730 GMT), and people protested against him shouting "Death to the hypocrite Mousavi."
Angry crowds then hit his car, banging their fists on the window pane, the report said, adding the opposition leader had to immediately leave the rally.
Iranian authorities, including Supreme leader Ayatollah Ali Khamenei, had warned the opposition against turning anti-Israel rallies to street protests against the clerical establishment.
Iran's June presidential election, which was followed by huge opposition protests, plunged Iran into political turmoil and exposed deepening divisions within its ruling elites.
The opposition leaders say the poll was rigged to secure Ahmadinejad's re-election. The authorities deny it.
Denying the Holocaust
As part of the official anti-Israel day, Ahmadinejad raised the stakes against Israel by describing the Holocaust as a lie, just as world powers are trying to decide how to deal with the nuclear ambitions of an Iran in political turmoil.
"The pretext (Holocaust) for the creation of the Zionist regime (Israel) is false ... It is a lie based on an unprovable and mythical claim," he told worshippers at Tehran University at the end of an annual anti-Israel "Qods (Jerusalem) Day" rally.