Greece has resumed deportations of refugees and migrants from its islands to Turkey after a four-day pause, sending back 124 people on two boats from Lesbos to a port on the Turkish coast.

Before the first boat left the island, four activists jumped into the sea to try to obstruct the operation - swimming to the front of the chartered ferry and grabbing the anchor chain - and were detained by the coastguard.

The migrants were placed on the boats by officers from the European Union's border protection agency and taken to the Turkish port of Dikili where health and migration officials checked the passengers amid heavy security.

After the checks, the migrants were whisked on to police-escorted buses.

An agreement between Turkey and the European Union came into full effect on Monday when 202 migrants were sent back.

About 4,000 migrants and refugees who reached Greek islands from nearby Turkey after March 20 are being held in detention camps to be screened for deportation.

The returns have been held up by delays in processing asylum claims by overwhelmed Greek authorities who are also preparing to deal with applications across the country by 50,000 stranded migrants and refugees promised places in a slow-moving EU relocation scheme.

On Greek islands, protests continued at overcrowded detention camps.

Police cleared the main port on the island of Chios overnight, where scores of migrants had been camped out for a week after pushing their way out of a detention camp. Scuffles occurred between police and Greek protesters staging rival demonstrations at the port in support of and in opposition to the migrants there.

Amnesty International said migrants were being held "arbitrarily in appalling conditions" at camps on Chios and Lesbos, after interviewing dozens of detainees there.

"On the edge of Europe, refugees are trapped with no light at the end of the tunnel," Amnesty's deputy Europe director Gauri van Gulik said.

"A set-up that is so flawed, rushed and ill-prepared is ripe for mistakes, trampling the rights and well-being of some of the most vulnerable people."

A Turkish official said his country is prepared to receive higher numbers with an array of 1,000 professionals ranging from doctors to migration officials and police deployed in Dikili.

The official said they expected to receive 2,050 migrants on Friday.

He said those returned Friday were primarily Afghan and Pakistani nationals. There were also four Iraqis and one each from Egypt, Morocco, Bangladesh and the Palestinian territories. All are to be processed for deportation within two weeks.

Returns from Greece to Turkey are expected to resume next week, according to the Turkish official.

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