The charges came on Wednesday as Mousavi again rejected the results of the June 12 vote which authorities confirmed for the second time earlier this week.
The authorities said 17 protesters and eight Basiji were killed in two weeks of unrest that followed the election.
Mousavi, who contends that there was widespread fraud in the election and insists he was robbed of victory, continues to describe Iran's government as illegitimate and has called for electoral reform.
In a statement on his website on Wednesday, Mousavi said he and his supporters would not recognise the legitimacy of a future government run by Ahmadinejad.
"From now on, we will have a government the legitimacy of which the majority of the people, including me, will not acknowledge," he said.
"Our historic duty is to continue the protests to defend the rights of the people... and prevent the blood spilled by hundreds of thousands of martyrs from leading to a police state."
Mehdi Karoubi, a cleric and fellow losing candidate, echoed Mousavi's allegations and unleashed fierce attacks on the election outcome, calling for it to be annulled.
'Not too late'
Iran's Guardian Council on Monday officially confirmed the re-election of Mahmoud Ahmadinejad as Iran's president for a second term, following a partial recount of votes.
The council agreed to the partial recount after defeated candidates alleged that Ahmadinejad's declared victory was due to "rigged" voting.
State television on Monday said that Ayatollah Ahmad Jannati, the council's secretary, had presented Sadegh Mahsouli, the minister of the interior, with a letter saying it had approved the election after a recount of 10 per cent of the ballots.
But Mousavi said the Guardian Council had "closed its eyes to numerous irregularities".
"It is not too late and it is still possible to restore the people's trust ... the safety of our system depends on doing this," he said, addressing the Guardian Council.
The disputed vote unleashed the worst unrest seen in Iran since the 1979 revolution, sparking violent clashes between protesters and police and resulting in the deaths of at least 20 people.
Ismail Ahmadi-Moghaddam, Iran's police chief, said more than 1,000 people were arrested in the wave of protests.
"No policeman was killed in the Tehran riots but 20 rioters were killed," the Fars news agency quoted him as saying.
"Police arrested 1,032 people in the recent riots. Many have been released and the rest are being prosecuted in Tehran's public and revolutionary courts."
While calm has returned to Tehran's streets, the country continues to be embroiled in diplomatic spats.
European diplomatic sources said on Wednesday that EU members were considering a proposal from Britain to recall all their ambassadors from Iran in protest at the detention of its Tehran embassy employees.
The threat was made as Britain said that two more employees from its embassy had been released.
Iran's state-run Press TV said just one of the nine local staff members detained was still in custody.
Iranian authorities released five British embassy employees on Monday.
Relations between the countries have been strained since Tehran accused Western powers - mainly Britain and the US - of inciting street protests and violence following the election, charges both nations rejected.