The Greek government has asked ferry operators to reduce services bringing migrants from islands to the capital Athens in a bid to ease pressure.
It is trying to slow the flow of migrants to its northern border, to prevent a further build-up of people trying to reach other EU states.
Countries further north have imposed border restrictions that make it harder for arrivals to move on from Greece.
About 2,800 people massed on Greece’s border with Macedonia on Thursday.
Only 100 were allowed to cross, correspondents say.
The camp at Idomeni is above capacity, and more people are waiting nearby.
EU migration: Crisis in graphics
Last weekend, Macedonia barred entry to Afghans at its border with Greece. Angry protests erupted at the border crossings and Greece was forced to transport hundreds of Afghans back to Athens.
Thousands of people continue to land on Greece’s islands every week, having made the risky crossing from Turkey.
Meanwhile, a row between Greece and Austria, one of the countries that has tightened its border security, has deepened, with Athens snubbing a request to visit by the Austrian interior minister.
Johanna Mikl-Leitner had warned that if Greece could not secure the external borders of the EU, then other countries would have to take action.
Around 2,000 migrants arrived at the port of Piraeus, near Athens, on Thursday alone.
However, many cannot now travel further north, and the numbers stuck in Greece are building.
In northern Greece, protesters blocked the entrance to a new proposed camp for migrants near Polykastro.
Some local people said they were concerned that the camp would become permanent.
The government minister responsible for shipping, Theodoros Dritsas, told Mega TV the plan was “a controlled deceleration of refugee movement and flow of immigrants from the islands to the port of Piraeus”.
The aim was to create “new temporary residence areas in Attica [the Athens region] and other parts of the country to address the consequences of the closure of the border,” he said.
The government had asked that three ships serve as temporary hotels for the refugees and migrants for two or three days, before taking them to Piraeus.
However the government would not create a “non-manageable” situation on the islands, Mr Dritsas said.
The plan particularly affects Lesbos, Chios and Samos, islands which are close to Turkey.
The Catholic humanitarian organisation Caritas tweeted that Thursday night’s ferry from Lesbos had not departed, “leaving refugees and migrants stranded”.
The island risked becoming “one big camp if refugees and migrants continue to arrive without any option to leave,” it said.
Greece had already recalled its ambassador to Austria on Thursday amid sharp divisions among EU states over the migrant crisis.
It acted after Austria hosted a meeting on the migrant issue with Balkan states, to which Greece was not invited.
The Athens government has been criticised by other EU countries for failing to manage the new arrivals – but no progress has been made on a European plan to relocate refugees from Greece.
Prime Minister Alexis Tsipras has threatened to block all decisions at EU migration summits next month if member states do not agree to take in quotas of migrants.
A note on terminology: The BBC uses the term migrant to refer to all people on the move who have yet to complete the legal process of claiming asylum. This group includes people fleeing war-torn countries such as Syria, who are likely to be granted refugee status, as well as people who are seeking jobs and better lives, who governments are likely to rule are economic migrants.