Censor.NET reports citing Daily Mail referring to AP.
Foreign Ministry spokesman Martin Schäfer said Honcharenko's actions constituted "wholly inappropriate behavior."
Schäfer said Germany considers a Ukraine a "close partner" and was the first country to establish diplomatic relations with Kiev 25 years ago.
He said Germany is working to host a meeting of foreign ministers from Ukraine and Russia next week.
As previously reported, Honcharenko defaced a fragment of the Berlin Wall at the German embassy in Kyiv in protest against the German Ambassador Ernst Reichel's suggestions about local elections in the Donbas.
The embassy said the act was in violation of the Vienna Convention on Diplomatic Relations.
Earlier, Reichel said in an interview it was not necessarily that elections in the Donbas take place only when there are Russian troops or Ukrainian flag is posted on each city administration.
As an example, the ambassador cited the last 1990 parliamentary elections in the German Democratic Republic, which took place in the presence of Soviet troops.
Ukraine's Foreign Ministry has summoned Reichel in connection with the incident.