Migrants rescued by NATO vessels in the Aegean Sea will be returned to Turkey, Secretary General Jens Stoltenberg said early Thursday after the military alliance finalized an operation to monitor the smuggling networks that help people reach Greece.

NATO agreed two weeks ago to help combat the flow of migrants to Europe in response to a request by Turkey, Greece and Germany. But work to agree the details of the operation ran into difficulties after Ankara signalled reluctance to take back anyone rescued at sea.

Europe has been struggling to deal with a surge in migration that saw more than 1 million people arrive in 2015. Many are asylum seekers fleeing the war in Syria, but economic migrants have also joined their ranks.

The short sea passage across the Aegean has been their main crossing point to Europe, but has claimed several hundred lives this year.

"We will participate in international efforts to cut the lines of illegal trafficking and illegal migration in the Aegean Sea. Because this crisis affects us all," Stoltenberg said in a statement issued early Thursday.

"NATO's task is not to turn back the boats," the NATO chief said, while adding that its vessels had a responsibility to rescue people in distress at sea, as does any boat under international law.

"In case of rescue of persons coming via Turkey, they will be taken back to Turkey," Stoltenberg added.

NATO vessels arrived in the Aegean last week, and are carrying out reconnaissance, monitoring and surveillance activities, the NATO chief said, adding that the alliance is also establishing direct links with the European Union's border agency Frontex.

The aim of the operation is to feed information to the national authorities in Greece and Turkey, to help them crack down on human trafficking and criminal networks fuelling the migration crisis.

Four vessels under German command, including personnel from Canada, Greece and Turkey, were rerouted last week from another part of the Mediterranean Sea, according to NATO officials.

Participating NATO vessels can operate in Greek and Turkish waters, but Ankara and Athens have agreed not to send forces into each others' waters or airspace, Stoltenberg said. The two sides are embroiled in a long-running territorial dispute.

He noted that NATO is uniquely placed to facilitate the cooperation and exchange of information between Greece and Turkey, as both countries are members of the alliance, while only Greece is in the EU.

Stoltenberg's comments came hours before a meeting Thursday of EU interior ministers in Brussels to discuss joint efforts to curb the migrant inflow.

Turkish Deputy Interior Minister Sebhattin Ozturk was also due to join the talks, as well as representatives from countries along the Western Balkan migration route and UN High Commissioner for Refugees Filippo Grandi.

Athens is angered by Europe's handling of the crisis, with countries further along the migration route restricting access, leading to backlogs of migrants and asylum seekers in Greece.

Greece was further irked by its exclusion from a conference Austria held Wednesday in Vienna with Western Balkan nations where additional border filters for migrants were agreed.

Prime Minister Alexis Tsipras threatened late Wednesday to block EU decision-making until an agreed scheme to redistribute asylum seekers across the bloc is implemented.

So far, just a fraction of the 160,000 arrivals that are supposed to be relocated to other member states have been moved under the scheme agreed last year.

Since non-EU member Macedonia, backed by Austria and other members, squeezed its border gates further shut on Sunday, thousands of migrants have massed in Greece from Athens to the border 600 kilometres north.

Tsipras on Wednesday night described the situation as "shameful," promising that he will not allow Greece to turn into a migration buffer.

The Greek prime minister received support from German Foreign Minister Frank-Walter Steinmeier, who told the daily Rheinische Post that it was "an illusion" to believe a solution to the crisis was possible without Greece.

Europe needs the countries on its frontier to control the influx of refugees, Steinmeier said.

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