"What has happened has satisfied some and angered many others, but this anger should not push people not to take part in the elections," the embattled president said on Monday in a statement carried by the official news agency IRNA.
"Many people have the feeling that in many constituencies, they cannot vote for their preferred candidate. But with a little tolerance, they can search to find those candidates who are closest to their views," Khatami wrote.
"Even if they cannot send the person they want to the Majlis, they can prevent those they do not want from entering," he added.
In a clear reference to religious hardliners, he warned that
"non-participation in elections would allow a minority to take
control of the destiny of the country."
"Nobody can force our people from adhering to a point of view
they do not believe in, but at the same time one cannot not
participate in the elections ... even if the people, the candidates and the deputies have been mistreated."
He called on voters to "choose the best possible candidate", but admitted he was "writing with a heavy heart".
"We must fight with all our strength to defend religious
democracy," said the president.
Iran's conservatives are expected to oust reformists from the
parliament after a hardline political watchdog, the Guardians
Council, disqualified some 2300 candidates from even standing. Most on the blacklist are reformists.
The reformist camp behind Khatami is now in disarray, with the main party led by the president's brother boycotting the polls and the remaining moderate groups only able to contest around 200 of the 290 seats up for grabs on Friday.
"We must fight with all our strength to defend religious democracy"
But while there is little choice for reformists, plenty of conservative blocs are standing - ranging from pragmatic members of the centre-right to minority Islamic extremists.
The campaigning, due to end at midnight on Wednesday, has been marked by widespread apathy.