"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 on Thursday 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.
The premier championed a March deal with the EU, brokered by Germany, to stem the flow of refugees across the Aegean Sea - an accord in which the president has shown little interest despite Turkey being on the verge of winning visa-free travel to Europe for its citizens.
Erdogan on Friday said that he would refuse to bow to EU demands that he reform terrorism legislation, one of 72 criteria Turkey must meet for the deal to go ahead.
"We will go our way, you go yours," he said in a speech directed at EU leaders.
Fears in Germany
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.
A senior member of Merkel's Christian Democratic Union party, Norbert Röttgen, called the reshuffle "bad news for Europe and Turkey".
"Davutoglu wanted to move Turkey toward Europe on all issues that are important for Europe," he told German public radio. "Erdogan is dead-set against that."
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 Günter Burkhardt told AFP.