The visit comes amid questions over the legality of the EU-Turkey pact, which deports back to Turkey refugees who do not qualify for asylum in Greece.
However, human rights groups say Turkey is not a safe place to return people.
Turkish officials have warned the deal could collapse if demands for visa-free EU travel for its citizens are not met.
The agreement says Turkey must meet 72 conditions by May 4 to earn the visa waiver, but diplomats say only half of those points have been met so far.
Angela Merkel is expected to visit a refugee camp in the southern city of Gaziantep, near the Syrian border, where she will meet Turkey’s PM Ahmet Davutoglu.
The German chancellor will travel with the European Council President, Donald Tusk, and the EU Commission Vice-President, Frans Timmermans.
Angela Merkel has faced opposition in Germany for her migration policies and has defended the deal with Turkey despite opposition from some European partners.
Her trip comes as she faces additional pressure for agreeing to the prosecution of German comedian Jan Boehmermann accused of insulting Turkish President Recep Tayyip Erdogan.
Advocates of freedom of speech in both Turkey and Germany have called on Angela Merkel to send out a strong message on the issue during her visit.
The goal of the EU-Turkey deal is to deter refugees, mainly Syrians and Iraqis, from making the crossing between Turkey and Greece.
Under the agreement, refugees who have arrived illegally in Greece since March 20 are expected to be sent back to Turkey if they do not apply for asylum or if their claim is rejected.
For each Syrian migrant returned to Turkey, the EU is due to take in another Syrian who has made a legitimate request.
The scheme has reduced sharply the number of arrivals, from more than 56,000 in February to around 7,800 over the past 30 days, according to the European Commission.
However, the International Organization of Migration said unofficial data for arrivals in Greece in recent days suggested the numbers were picking up again.
The promised relocation to EU countries seems to be slow as nations are reluctant to take in more refugees – 103 Syrians have been resettled from Turkey to Europe, the commission said.
In March 2016, EU border agency Frontex requested 1,550 extra staff to help oversee the deal, but so far only 340 police officers and experts have been sent.
Rights organizations have attacked the scheme, with Amnesty International saying that Turkey has illegally returned Syrians to their country, a charge Ankara denies.
The EU has pledged up to $6.8 billion in aid to Turkey over the next four years.
Ankara, however, expects more, including visa liberalization, a point which faces opposition of some EU members.
President Recep Tayyip Erdogan said earlier this month: “If the European Union does not take the steps it needs to take, if it does not fulfill its pledges, then Turkey won’t implement this agreement.”
Turkey already hosts some 2.7 million Syrian refugees, at a cost of over $10 billion, the government says.
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