The troops and planes participating in the international coalition against the Islamic State group will redeploy to Jordan. Merkel portrayed the move as allowing Germany and Turkey to put aside one of many problems causing friction between the two NATO allies.
Germany has about 270 troops stationed at Incirlik, near the Syrian border, with six Tornado reconnaissance aircraft and a refuelling plane.
It pledged to do what it can to limit disruption caused by the move to a base in Jordan. The Defence Ministry said that the relocation would take the refuelling plane out of service for two to three weeks, and the reconnaissance planes for two to three months.
German deployments abroad require parliamentary approval, and German leaders say it's essential that lawmakers be able to visit troops when they want.
Turkey blocked the latest Incirlik visit request in anger over German authorities' decision to grant asylum to soldiers and other individuals that Turkey accuses of participating in last year's failed coup.
A previous standoff over Incirlik last year was eventually resolved. But Germany's foreign minister failed to break the current impasse during a visit to Ankara Monday. Ties have also been soured by issues such as the jailing in Turkey of two German journalists and by German local authorities banning planned campaign rallies by Turkish ministers earlier this year.
"We can then concentrate in our talks on other issues," she said. "There are enough difficult things, but I don't see in this step a situation in which things have worsened." Pointing to issues such as migrant flows and economic ties, she said that Germany has many "common interests" with Turkey and the two countries need to keep talking.
Germany's defence minister called Turkish counterpart Fikri Isik to thank Turkey for hosting the troops and inform him of the decision, Turkish officials said. Isik said care would be taken so that the withdrawal doesn't affect the fight against IS, according to defense ministry officials who spoke on condition of anonymity in line with Turkish regulations.
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