Refugees and other migrants pouring into Greece will be kept on Aegean Sea islands on ferries used as floating shelters, government officials said, as thousands who went before them find themselves stranded in increasingly desperate conditions following border closures in the countries to the north.

Ferry companies and authorities on Greek islands have been instructed to limit the number of migrants travelling by ferry to the mainland, where thousands have been sleeping rough in parks and along the country's highways, with existing shelters filled to capacity.

In Athens, migrants staged peaceful protests, briefly blocking traffic at the country's main port in nearby Piraeus, while hundreds walked out of a transit camp and were heading by tram and on foot to join others at the port.

"We hoped to get to Germany and all the people around here are looking to get to Germany," Afghan migrant Muchtar Ahman said, speaking at a central Athens square where he was camped out with friends.

We are hopeless, we are homeless

"But when we came here the borders, the Macedonian borders closed, we are really disappointed. We are hopeless, we are homeless."

Merchant marine minister Theodoros Dritsas said up to two-thirds of migrants arriving on Lesbos and other Greek islands would be held there until Sunday.

"The reason is that we need more time to prepare additional sites for temporary shelters," Mr Dritsas said.

He said three chartered ferries - with a combined capacity of about 4,000 places - would be used on islands to provide temporary shelter over the next three days.

About 2,000 people - more than half from Syria and Iraq - are arriving daily from Turkey using dinghies and small boats, but the number of people crossing into neighbouring Macedonia has dropped dramatically in the past week, and was down to just 150 on Thursday, according to Greek police figures.

By early Friday afternoon, not a single migrant had crossed into Macedonia, while some 4,500 people waited at a border camp and a nearby site, according to Greek police.

In Serbia, police said they had been formally notified by Croatia and Slovenia that only 500 people per day would be accepted to cross the border northward.

In Munich, German chancellor Angela Merkel stressed the need for a unified European approach to tackle the migrant crisis and said she was encouraged by the recent deployment of Nato ships in the Aegean alongside vessels from the European Union border agency Frontex.

"Nato has started to work in collaboration with the Turkish coast guard and Frontex. It is too early to see the effects of this measure. All 28 (EU) member states want to stop illegal immigration," she said.

But Nato secretary-general Jens Stoltenberg, in an article posted on the alliance's website, said the ships would only be providing a support role.

"Nato ships will not do the job of national coastguards in the Aegean. Their mission is not to stop or turn back those trying to cross into Europe. And this in no way represents a militarisation of the response to the crisis," he wrote.

Athens is blaming Austria - a fellow member of Europe's passport-free Schengen Area - for the flare-up in the crisis. It imposed strict transit restrictions last week, controls that were also implemented by Balkan countries further back on the route.

Greece recalled its ambassador to Austria on Thursday and rejected a request to visit Athens by Austrian interior minister Johanna Mikl-Leitner, government officials said.

Athens says it is unable to stop migrants crossing its sea borders without endangering their lives.

"The policies of Austria and Hungary are turning Greece into a giant refugee camp," deputy education minister Sia Anagnostoipoulou told state-run ERT television.

"What are we supposed to do: Let people drown in the Aegean Sea?" she said. "Instead of making a plan, Europe is burying its head in the sand ... Europe is unravelling."

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