Greece said authorities would start ruling on asylum applications from hundreds of migrants and refugees in the next two weeks, in a major test of a new deal to try to control the flow of people desperate to reach Europe.

By the latest count, more than 50,000 people, most from Syria, Iraq and Afghanistan, have been stranded in Greece since Balkan countries closed their borders in February to migrants and refugees wanting to cross, mostly on the way to Germany.

Many of them are refugees from war, but others are economic migrants.

Asylum applications have been piling up since March, when the European Union and Turkey signed an agreement intended to close off the main route into Europe, has seen an influx of over a million refugees and migrants since last year.

Under the EU-Turkey deal, those who arrive to Greece from 20 March will be screened, registered and detained in holding centres until their asylum applications are processed.

Rejected applicants, and those who do not apply, are returned to Turkey.

Amnesty International has called the situation in Greece "very chaotic," without enough attention for individual processing and has voiced concerns that the process will be a "rubberstamping exercise" to send people back.

So far, around 325 people who did not request asylum have been returned from the Greek islands under the accord, which the UN refugee agency (UNHCR) has condemned and rights advocates say may violate international law.A spokesman for the European Asylum Office (EASO), a partner in implementing the deal, said the time frame was "feasible".

EASO officials have been deployed on the island of Lesbos since last week carrying out "admissibility assessments" of arrivals.

Most of the 50,000 stranded in Greece arrived before 20 March and are not subject to being returned under the latest deal.

Their fate remains unclear, however some are expected to be moved to other European countries under relocation plan agreed many months ago.

More than 11,000 live in tents in a makeshift camp near the town of Idomeni on the Greek-Macedonian border, where clashes broke out on Sunday after a group tried to storm the border fence.

The government has blamed unidentified "activists" for instigating attempts to cross the border.

A spokeswoman said authorities were monitoring the activities of such individuals and were distributing leaflets to those camped at Idomeni asking them to not believe "rumours and false information given out irresponsibly by strangers.

A police official in northern Greece told Reuters 16 people, mainly EU nationals, were briefly detained and that the force was carrying out precautionary checks on those approaching the camp to avoid "dangerous situations or the transportation of dangerous goods."