"In view of the declarations, which we found disconcerting, we have invited the Iranian ambassador to the foreign embassy this afternoon where we will ask him for an explanation, a clarification," spokesman Andreas Peschke said.
He stressed however that it was an "invitation" and that the Islamic republic's ambassador was not being "summoned."
"What we are talking about is a clarification," Peschke told a regular government news conference, adding that similar meetings were set to take place in Paris and in London.
German Chancellor Angela Merkel called on Sunday for a recount in Iran's presidential election, which according to official results was won by the hardline incumbent, Mahmoud Ahmadinejad, by a large margin.
"We will not allow ourselves to be intimidated by Iran," the parliament's liason for foreign affairs, Gernot Erler, told public radio.
Meanwhile the German Foreign Ministry on Monday urged citizens to avoid non-essential travel to Iran, following earlier action by Britain and Italy.
Berlin urged individuals and groups to try to postpone planned trips and also warned Germans in Iran to "avoid large gatherings and political assemblies," under new guidlines posted on the ministry's website.
Riot police armed with clubs and riding motorbikes fired tear gas at about 1,000 opposition protesters in the Iranian capital after they defied an official ban on demonstrations.
Iran's Revolutionary Guards, an elite force set up to protect the Islamic republic in the wake of the 1979 revolution, warned on Monday it would crush further demonstrations over the disputed presidential election.
The warning came after state radio said at least 457 people had been detained in street clashes in Tehran on Saturday that left 10 people dead, bringing the overall toll from a week of violence to at least 17.
Iranian leaders have lashed out at "meddling" by Western nations - particularly the United States and Britain - and accused the foreign media, already facing tight restrictions on their work, of fomenting the unrest. British Foreign Secretary David Miliband has rejected the accusations, and denounced what he said were Iran's effort to turn the election dispute into a "battle" with the outside world.
French Foreign Minister Bernard Kouchner condemned what he called "this brutal repression" while President Nicolas Sarkozy said the attitude of the Iranian authorities was "inexcusable."