"Strikes were carried out on targets of the Daesh (IS) terror group in Syria and the PKK terror group in northern Iraq," it said in a statement, saying shelters and warehouses containing PKK weapons were hit in the northern Iraq operation.
It listed seven locations in northern Iraq where the strikes had been carried out, including Mount Kandil where the PKK's military leadership is based.
Prime Minister Ahmet Davutoglu convened a meeting of top ministers and security officials early today at around 2:00 am (local time) in Ankara to discuss the cross-border operations, it added.
"Additional measures were agreed for the fight against terrorism and instructions given to the relevant authorities."
The military operations come after a week of violence in Turkey, including a suicide bombing blamed on IS and attacks on Turkish police claimed by the PKK.