"We call on the Iranian authorities to allow peaceful protests and stop using force, especially deadly force, against demonstrators," the Foreign Office said on social media.
German diplomats conveyed their concerns directly to the Iranian ambassador in Berlin on Monday, the ministry added.
Protests erupted across Iran after the death of a young woman who was taken in custody by controversial morality police in Tehran on September 13 for wearing an "improper" head covering. Iran says she died of a heart attack.