Passport control system in Istanbul Ataturk international airport departure terminal and another airport in the City was affected.
A flight to Libya was cancelled and a dozen other were reported delayed before authorities restored the system mid-afternoon.
Responsible authorities believe those systems were hit by malwares. They are also investigating if those malwares got user details from infected machines.
There is no claim of responsibility or blame was attributed to the alleged cyberattack local media report says.
Cybersecurity has emerged as an emerging threat to national security in the digital age.