Turkey says can't take new migrant wave from Afghanistan
President Erdogan meets people during a visit to the flood zone.
"Turkey, which already has five million refugees, cannot take an additional burden of migrants," he told Merkel.
Erdogan made similar comments to Greek Prime Minister Kyriakos Mitsotakis on Friday.
The EU also pledged to work with Ankara on upgrading an existing customs union and on paving the way for Turkey's eventual accession to the bloc.
Turkey further wants visa-free travel to EU nations and the resumption of regular summits between the two sides.
But Ankara has regularly accused the EU of not keeping to the terms of the accord.
Merkel's office, for its part, responded by saying that the evacuation of people from Afghanistan remains "the top priority".
The two leaders agreed to "close cooperation to support the work of international organisations, in particular UN refugee aid agencies, in Afghanistan and in neighboring countries," said a spokeswoman for Merkel.