Greek Defence Minister Panos Kammenos criticized what he called Turkey's "cowboy antics".
"We want peace, we are not looking for a fight or for trouble in the Aegean, but there won't be an aircraft which will not be intercepted," Kammenos told Antenna Television.
A Greek court last week blocked the extradition of eight Turkish military officers Ankara accuses of involvement in a failed coup in July 2016. Turkey said relations between the two countries would be reviewed.
Turkey and Greece, members of the NATO military alliance, came to the brink of war in 1996 over the ownership of uninhabited islets known as Imia in Greek and Kardak in Turkish.
A statement by a Greek deputy shipping minister in early January on plans to make 28 small Aegean islands habitable stoked Ankara's ire.
"Greece is trying to take advantage of Kardak and similar rocky areas. Greece will not be permitted to open new areas here," Turkish Deputy Prime Minister Veysi Kaynak said during a roundtable interview with reporters on Wednesday.
On Sunday, Turkey's chief of staff and the heads of the navy, air force and land forces went to inspect a naval headquarters and passed close to Kardak, the military said in a statement.
On Wednesday, Kammenos flew by helicopter over the region and threw a wreath into the sea to commemorate three Greek officers who died in a helicopter crash during the 1996 crisis.
"It was my obligation to be there ... I won't ask for anyone's permission," he said.
(Reporting by Michele Kambas, Renee Maltezou and Humeyra Pamuk; editing by Andrew Roche)