"The cancellation of Mahan Air airline's authorization to fly to Germany is a hasty and unjustified step. It is inconsistent with the spirit of relations existing between the two countries," Qassemi said, as quoted in the ministry's Telegram channel.
He also said that the decision was not compliant either with German or with Iranian interests.
Qassemi suggested that the move could be motivated by "fake information" spread by some party "displeased" with the Iranian-German relations.
The spokesman expressed hope that the German authorities would review their decision.
On Monday, the German Transport Ministry announced that Mahan Air had been barred to fly to and from Germany, while a spokesman for the German Foreign Ministry added that the decision had been taken to safeguard the country's "security interests."
The US Treasury barred citizens from flying with Mahan Air and froze its assets in the country in 2011 for its alleged aid to Iran’s Revolutionary Guard Corps and the Lebanon-based Hezbollah. On Monday, US Secretary of State Mike Pompeo praised Berlin's decision and called on other countries to bar the airline from their airspace.