The Turkish military said on its Web site Sunday that two F-16 jets had violated Turkish airspace for four minutes on May 24, crossing the Iraqi border into Turkey's region of Uzumlu, in the province of Hakkari.
U.S. officials have said the crossing was inadvertent.
A U.S. Embassy official was handed a protest note at the Foreign Ministry on Tuesday, said ministry spokesman Levent Bilman. Turkey asked that such incursions do not take place again, Bilman said.
A U.S. Embassy official said the diplomat told Turkish officials that the incursion was a pilot error and that steps would be taken to prevent it from occurring again. The official spoke on condition of anonymity in line with embassy rules.
The airspace violation came amid intensified debate in Turkey about whether to stage a military incursion into northern Iraq to hit Kurdish rebels bases in the region. It raised speculation in Turkey that the U.S. was spying on the Turkish military's possible preparation for a cross-border offensive.
Turkish media have been reporting that the army was massing troops and tanks along the border, including in Uzumlu.
Prime Minister Recep Tayyip Erdogan said this week he would back Turkey's generals if they decide to strike Kurdish rebels in Iraq.
The U.S. opposes Turkish military action, which Washington fears could destabilize northern Iraq, the calmest part of the country.
Predominantly Muslim Turkey and the U.S. have historically close ties and possess the two largest militaries in the NATO alliance.
However, the two countries are still trying to repair relations strained in 2003, when Turkey refused to allow the U.S. to launch operations for the war in Iraq from Turkish soil. Ankara believes that regional instability caused by the U.S.-led war in Iraq are harming Turkish interests.
Ankara has repeatedly expressed its disappointment with the U.S. for what it says is the failure to crack down on Kurdish rebels who take refuge in northern Iraq and frequently attack soldiers and government targets in Turkey.
Turkey provides vital support to U.S. operations in Afghanistan and Iraq through Incirlik Air Base in southern Turkey, one of the most important U.S. military assets in the region.
The Kurdish rebel group, the PKK, has been fighting for autonomy since 1984 - a fight that has left tens of thousands dead. The group is considered a terrorist organization by the U.S. and the European Union.