Pro-government Basij members reportedly died in unrest over disputed June 12 poll results.
Under Iranian law, the punishment for people convicted as mohareb is execution.
Khatami’s comments came as the Guardian Council, Iran’s electoral watchdog, dismissed opposition allegations of fraud during the election.
The council said on Friday that the vote was the country’s “healthiest” since the 1979 Islamic Revolution.
“After 10 days of examination, we did not see any major irregularities,” Abbas Ali Kadkhodai, a Guardian Council spokesman, said.
“We have had no fraud in any presidential election and this one was the cleanest election we have had. I can say with certainty that there was no fraud in this election.”
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The statement leaves the opposition little room for further legal challenges over the election result, with the council previously rejecting a call for the vote to be annulled.
Supporters of Mir Hossein Mousavi, the main challenger to Mahmoud Ahmadinejad, Iran’s president, have led a series of mass demonstrations in the capital, Tehran, to protest against the results of the election.
At least 19 people are believed to have been killed in violent clashes between demonstrators and Iranian security forces.
Ghanbar Naderi, the economic and political editor of the state-owned Iran Daily newspaper, told Al Jazeera on Friday that the situation is now under control.
“Those who voted for Mr Mousavi in the capital have come to their senses now,” he said.
“They are slowly getting along with the reality that yes, most of them voted for Mr Mousavi in the capital, but the rest of the country voted for Mr Ahmadinejad.
“After two weeks … there are no violent demonstrations on the streets anymore and the last few people who used to take advantage of the situation have now been detained by the police forces and they will be put on special tribunal.”
War of words
The protests have also led to a war of words between Iran and the US, which has criticised the conduct of the June 12 election.
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Barack Obama, the US president, has warned that Tehran wanted to blame the US for opposition protests.
But Ahmadinejad, Iran’s president, called on Obama to “avoid interfering in Iran’s affairs” during a speech broadcast on Iranian state television on Thursday.
“This is our friendly advice; we don’t want to see the big disgraces of the Bush era to be repeated in the new US era,” he said.
Ahmadinejad’s speech came days after Obama said that he was “appalled and outraged” over threats, beatings and imprisonments of opposition protesters following the polls.
The latest comments by both presidents could complicate any attempt at a dialogue, which Washington hopes will include talks on the scope of Iran’s nuclear programme.