The strike killed two border guard battalion commanders and the driver of their vehicle, the army said in a statement.
It is the first time members of the regular Iraqi forces have been killed since Turkey launched a cross-border ground and air operation in mid-June against Kurdistan Workers' Party (PKK) rebels in the mountainous terrain of northern Iraq.
Iraq has already summoned the Turkish envoy in Baghdad twice in protest at Ankara's operations on its soil.
Ihsan Chalabi, the mayor of Sidakan in the north of Erbil province, told AFP that the drone had targeted "Iraqi border guard commanders while they were in meetings with PKK fighters".
Witnesses had reported clashes earlier in the day between PKK and Iraqi forces, and local sources said the drone strike targeted an emergency meeting called to try to calm the tensions.
At least five civilians have been killed since the start of the Turkish campaign in June.
Ankara has announced the death of two of its soldiers, and the PKK and its allies have reported the deaths of 10 fighters and supporters.
The PKK, which is blacklisted as a terrorist group by Ankara and its Western allies, has waged an insurgency against the Turkish state since 1984.
It has long used the rugged terrain of northern Iraq as a rear base to wage attacks on Turkey, which in turn had set up military positions inside Iraqi territory to fight them.
The Kurdish authorities, dominated by the Democratic Party of Kurdistan see the PKK as rivals but have never been able to uproot them from their northern Iraqi bases.