Her centre-right Christian Democratics may be opposed to the idea of Turkey joining the EU, but German Chancellor Angela Merkel has called for accession talks with Ankara to continue.
A meeting with Turkish Prime Minister Reccep Tayyip Erdogan in Berlin also touched on Syria’s civil war and the refugee crisis on Turkey’s border.
Negotiations to join the EU began in 2005 but have stalled over the issue of Cyprus.
Merkel said Brussels would pursue talks in good faith despite disagreements.
Ergodan took a swipe at Cyprus, the Mediterranean island which currently holds the EU rotating presidency, saying it should not have been allowed to join the bloc in 2004 because it was – and remains – split.
The Greek Cypriot south is recognised internationally while the northern Turkish Cypriot state is only acknowledged by Ankara.
Erdogan said it had been a “serious mistake” to accept Cyprus.
Around 2,000 people, many of them of Kurdish or Alawite origin, protested against his visit near the city’s Brandenberg Gate.
Some accused the Turkish leader of being a “dictator”, who they said had oppressed minorities and trampled on individual freedoms.
A recent EU report has also accused the government of infringing citizens’ rights.