Poroshenko told journalists at a joint briefing with Greek Prime Minister Alexis Tsipras, Censor.NET reports citing Ukrainski Novyny.
"Such a behavior of the people's deputy is absolutely inadmissible," he said.
The head of state also added that this was Honcharenko's personal opinion which was condemned by the faction as it did not reflect the position of the political force.
The Berlin Wall fragment was installed in Kyiv in 2009 to commemorate 20th anniversary of its fall.
As reported, Petro Poroshenko Bloc MP Oleksii Honcharenko painted a fragment of the Berlin Wall located at the German Embassy in Kyiv in protest against the German Ambassador Ernst Reichel's remarks on the elections in the Donbas.
Earlier, Reichel said in an interview that the elections in the Donbas don't have to be held only when there are no Russian troops or when the Ukrainian flag is flying over each city council building.
The ambassador cited the example of the last parliamentary elections held in the German Democratic Republic in 1990 in the presence of the Soviet troops.
About 30 members of the Verkhovna Rada reportedly urged Ukraine's Foreign Ministry to summon Reichel over his statements.
First Deputy Speaker of the Ukrainian Parliament Iryna Herashchenko also demanded explanations.
On the same day, the Foreign Ministry of Ukraine summoned Ambassador Reichel and explained him the inadmissibility of his statements about the possibility to hold elections in the Donetsk and Luhansk regions in the presence of the Russian troops.