The protesters broke into a conference center in Thessaloniki where the mayors of Greek and German cities met Wednesday and Thursday.
The name of the diplomat and any injuries he or she may have incurred were not reported.
The meeting came three days after Greek lawmakers approved an austerity budget of spending cuts and tax increases of about $12 billion for 2013. The vote occurred as about 20,000 demonstrators gathered outside parliament to protest the austerity measures.
On Thursday, the protesters were in Thessaloniki, demonstrating against the meeting between Greek and German leaders, the BBC reported.
"Studies show that 3,000 employees are required in Greece for local administration work carried out by 1,000 people in Germany," German Deputy Labor Minister Hans-Joachim Fuchtel said.
Protesters shouted "Nazis out" and "This will not pass" outside the conference center, and tried to prevent delegates from entering the building.
"These people haven't come here to help us, but to announce our death sentence," said Themis Balasopoulos, leader of Greece's municipal workers' union.