A boat carrying hundreds of migrants has capsized off the Greek island of Crete and a major rescue operation is underway, the Greek coastguard said Friday.

"The number of people in distress could be counted in the hundreds," a spokeswoman for the coastguard said.

"People are in the water, boats crossing the area have thrown lifebuoys and are moving to save the migrants."

She said a passing ship spotted the sinking vessel about 75 nautical miles south of Crete, Greece's largest island, in the southern Aegean Sea.

The coastguard rushed two patrol boats, a plane and a helicopter to the scene while at least four ships crossing the area joined the rescue operation.

About half of the 25-metre-long boat is underwater, the spokeswoman said.

It was not immediately clear where the boat had left from or where it was headed.

Some 204,000 migrants and refugees have crossed the Mediterranean to Europe since January, the United Nations refugee agency said on Tuesday.

It said more than 2,500 people have died trying to make the perilous journey this year.

The vast majority were killed crossing between Libya and Italy, as migrant arrivals to Greece have fallen sharply since the EU entered a controversial deal on March 20 with key transit country Turkey to stem the flow of migrants.

The Greek coastguard on May 27 intercepted a boat off Crete carrying 65 Syrian, Afghan and Pakistani migrants, and under the control of two suspected people traffickers -- a Ukrainian and an Egyptian.

The coastguard did not indicate if the boat, which the migrants said had left from Turkey, was headed for Italy or the smugglers had chosen the route through the southern Aegean to reach Greece by avoiding NATO ships deployed further north.

The NATO deployment is aimed at cutting off the Aegean Sea route used by hundreds of thousands of migrants to reached Europe since last year.