"We call for an end to the restrictions on Mr Morsi's whereabouts," a foreign ministry spokesman told reporters.
Morsi is currently being held in a "safe place, for his safety" and has not yet been charged with anything, according to the Egyptian foreign ministry, but military and judicial sources say he may eventually face charges.
The German ministry spokesman said a "trusted institution" such as the International Committee of the Red Cross should be granted access to Morsi.
And he called on all groups to refrain from violence as the Muslim Brotherhood, the influential group from which Morsi emerged, vowed to keep protesting until he is reinstated.
"We and our partners are of the opinion that any appearance of selective justice in Egypt must be avoided and there must be no political persecution," he said.
"That is not only an expression of our principles on the rule of law but also our conviction that any form of political persecution would be damaging for the future of Egypt."
He said "a return to democracy" in Egypt could only succeed "if all political forces can take part in the democratic transformation process."
The Muslim Brotherhood and opponents of Morsi have called separate rallies across Cairo Friday amid fears of further bloodshed in the Arab world's most populous country.