"The Chancellor has worked very well until now with Turkish Prime Minister (Ahmet) Davutoglu and all Turkish representatives and we assume that this good and constructive cooperation will continue with the new Turkish Prime Minister," German government spokesman Georg Streiter told reporters.
"The EU and Germany will continue to fulfil all their obligations under the agreement and we expect this from the Turkish side as well."
Davutoglu yesterday announced he would step down in two weeks as ruling party chief and premier, in a shock departure expected to further tighten President Recep Tayyip Erdogan's grip on power.
Davutoglu's impending departure sparked fears for the pact in Germany, which saw the biggest influx of asylum seekers in the EU in 2015 with more than one million people seeking refuge from war, persecution and poverty.
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A senior member of Merkel's Christian Democratic Union party, Norbert Roettgen, called the reshuffle "bad news for Europe and Turkey".
German refugee rights group Pro Asyl said it feared for asylum seekers in Turkey after Erdogan consolidated his power.
"The forced resignation of Davutoglu shows that Turkey is still miles away from being a country under the rule of law," its managing director Guenter Burkhardt said.