Greece on Wednesday said it had delivered a "strong protest" to Turkey after a helicopter carrying Prime Minister Alexis Tsipras was allegedly harassed by Turkish jets over the Aegean Sea.

"The foreign ministry delivered a strong protest to the Turkish ambassador," government spokesman Dimitris Tzanakopoulos told a weekly briefing.

In a further affront to Athens, the alleged incident occurred during Monday's celebrations of the start of the Greek war of independence from the Ottoman Empire in 1821.

Tsipras on Monday said his Chinook helicopter had been "forced into low-altitude manoeuvres" by Turkish warplanes "who violated our national airspace" before they were intercepted by Greek jets.

Tsipras had flown to the small island of Agathonissi, just off the Turkish coast, to mark the occasion.

"It seems they also wanted to participate in our national celebrations," he jibed.

"These senseless acts are meaningless. They are just wasting kerosene," Tsipras added. "The Greek PM will reach even the most isolated part of the country, even if he has to swim there."

Turkey has for decades disputed Greek sovereignty over Aegean waters and airspace close to Turkish shores, which Athens says is based on post-war treaties.

The two countries nearly went to war over a cluster of uninhabited islets in 1996, and mock dogfights between the two air forces are common.

Last year, a Greek fighter pilot died when his plane crashed in the Aegean while returning from a mission to intercept Turkish jets.