The EU says it is making plans to deal with a possible humanitarian crisis as new border controls halt migrants moving through the Balkans.
Greece has also expressed “displeasure” after the controls left thousands of migrants stranded in the country.
Thousands of migrants have been trapped in Greece after Macedonia barred entry to Afghans, days after Austria brought in new controls.
Latest figures show a huge rise in the numbers of migrants arriving in Europe.
The International Organization for Migration (IOM) says more than 100,000 asylum seekers have arrived so far this year, compared to fewer than 4,000 in the first two months of 2015.
Greece is the main arrival point for the migrants and refugees, having been smuggled across the sea from Turkey.
EU migration: Crisis in seven charts
“We are concerned about the developments along the Balkan route and the humanitarian crisis that might unfold in certain countries especially in Greece,” a joint statement by EU migration commissioner Dimitris Avramopoulos and Dutch migration minister Klaas Dijkhoff said.
“We call on all countries and actors along the route to prepare the necessary contingency planning to be able to address humanitarian needs, including reception capacities.
“In parallel, the commission is co-ordinating a contingency planning effort, to offer support in case of a humanitarian crisis both outside and within the EU, as well as to further co-ordinate border management.”
The head of the UN refugee agency (UNHCR) also warned on Tuesday that border closures in EU states would cause “further chaos and confusion”.
Filippo Grandi, visiting the Greek island of Lesbos where many migrants arrive, said it would increase the burden on Greece “which is already shouldering a very big responsibility”.
Greece expressed “displeasure” at the border restrictions, the office of Prime Minister Alexis Tsipras said, and also complained to the EU that it had not been invited to a conference on migration in Vienna on Wednesday which will be attended by Balkan states.
Austria has rejected the criticism.
On Tuesday, Greece began sending hundreds of Afghans back to Athens from its border with Macedonia.
Macedonia suspended all border crossings on Monday after Afghans staged a sit-down protest and occupied a railway line.
Macedonian police said Afghans had been stopped because Serbia, Croatia and Slovenia had “decided to reduce their numbers” and started sending them back to Macedonia.
“We can’t allow Macedonia to become a buffer zone and refugee camp,” a foreign ministry official was quoted as saying.
The move came two days after Austria controversially introduced a daily limit on asylum applications and on migrants travelling through the country.
Mr Avramopoulos has said the cap is “plainly incompatible” with Austria’s obligations under EU and international law.
European Commission President Jean-Claude Juncker also criticised the Austrian move, saying that “solo national approaches were not recommended”.
EU leaders have announced they will hold a summit in early March with Turkey to attempt to seek fresh solutions to the crisis.
Turkey is home to nearly three million refugees, most of them from Syria.
Many of them pay smugglers thousands of dollars to make the crossing to Greece. They then head north, trying to reach Germany and Scandinavia.
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.