Greece asked its passenger ferry companies and travel agencies on Friday to cut back on bringing migrants and refugees from frontline islands to the mainland and said its own chartered ships would stay put for a few days.

The moves, described by Greece's shipping minister as temporary, are designed to stem a flow of people mostly fleeing from violence in the Middle East, as border controls further north in the Balkans threaten to strand tens of thousands in Greece.

Most refugees arrive in the European Union after a short but at times dangerous journey by small boats from Turkey to nearby Greece islands such as Lesbos.

At least 20,000 refugees and migrants have been stranded in Greece after border shutdowns through the Balkans route to central and northern Europe.

Greece on Thursday recalled its ambassador to Austria in anger over the border closures and has threatened to block European Union decision-making unless the bloc comes up with concerted action to deal with the crisis.

"We have taken some actions because of border closings, including an increase of temporary shelter spaces and a relative slowdown of the transport of migrants from the islands to the port of Piraeus," Shipping Minister Thodoris Dritsas told Skai TV.

He said three ships chartered specifically to move migrants to the Greek mainland would be docked at the islands and accommodate refugees for 'two or three days'.

"It is a small scale slowdown (of flows to the mainland)," he said.

Greece has been unable to contain thousands of refugees at registration camps, with hundreds taking to the nation's highways to walk towards the northern border it shares with Macedonia. Some were sleeping rough in central Athens, and others in stadiums.

Macedonia, to the immediate north, is accepting only Iraqis and Syrians, witnesses say, with Afghans being turned back. There were an estimated 2,500 people amassed at Idomeni, the border area with Macedonia early Friday, with hundreds more on their way.