A senior cleric told opposition leaders to repent or be declared enemies of God and face death.
Just hours later, state news agency IRNA reported that top opposition leaders Mir Hossein Mousavi and Mehdi Karroubi had fled the capital fearing for their lives.
An opposition website said the two men had been taken into custody by members of the elite Revolutionary Guards and intelligence ministry for their own protection.
'Two of the chiefs of the sedition left Tehran for the north of Iran after learning that the population was increasingly angry and demanding their punishment,' IRNA said.
They were said to be in the locality of Kelar-Abad, in Mazandaran province, due north of Tehran on the Caspian Sea.
Opposition website Rahesabz said: 'Members of the Revolutionary Guards and the intelligence ministry picked up Mousavi and Karroubi in the city of Kelar-Abad to protect them from the anger of the people.'
There was no official confirmation that the pair were in custody.
Earlier, television footage showed crowds in areas including Tehran's Enghelab Square chanting slogans and waving pro-regime placards.
The rallies were called in response to a series of opposition protests against President Mahmoud Ahmadinejad's disputed June re-election.
Mir Hossein Mousavi and Mehdi Karroubi were the main challengers in that poll.
Hardliners have reacted angrily after thousands of opposition supporters used Sunday's climax of Ashura, one of Shia Islam's holiest days, to protest, condemning the demonstrations as 'desecration'.
'The offensive slogans have made the pious Iranian nation sad and the Zionist world happy, and in practice they as pawns of the enemies have furnished a red carpet for the foreigners who are aiming at the nation's security,' the government said.
Public prosecutor Gholam Hossein Mohseni Ejeie told a closed session of parliament that Mir Hossein Mousavi and Mehdi Karroubi 'are on the wanted list', ILNA news agency reported, citing MP Hassan Norouzi.
And in some of the strongest language since the election, a senior conservative cleric told opposition leaders to 'repent' or be declared 'enemies of God' and face the death sentence.
Without naming anyone, Ayatollah Ahmad Alamolhoda told a Tehran rally that 'millions of people here are telling the heads of the sedition that since the supreme leader still keeps open the gate of repentance for you, then in a deadline that should be set by the judiciary you must repent and return to the path of the leader.'
