Thousands of refugees could be left in "legal limbo" as European countries adopt different border rules to deal with the record influx of migrants, the UN refugee agency (UNHCR) has warned.
It has called for the establishment of big European-run reception centres in countries where migrants are arriving.
The statement came as Germany imposed controls on its border with Austria.
European interior ministers are to hold an emergency meeting on the migrant crisis later on Monday.
Ministers are due to vote on a plan to redistribute an initial 40,000 asylum seekers through mandatory quotas, though Central and East European states have opposed this.
The EU has since raised the number of people it seeks to share out through quotas to 160,000 asylum seekers across 23 EU states.
Europe as a whole is struggling to deal with an enormous influx of people, mostly from Syria but also Afghanistan, Eritrea and other countries, fleeing violence and poverty.
Many migrants have been refusing to register in countries such as Greece or Hungary, fearing it will stop them being granted asylum in Germany or other EU states.
The UNHCR said it was concerned that migrants seeking protection they are entitled to could "find themselves moving around in legal limbo".
It said that recent successive announcements of different border control measures by a number of European countries "only underlines the urgency of establishing a comprehensive European response".
This response must be based on the creation of effective reception centres which would "properly assist, register and screen people upon arrival in Greece, Italy and Hungary".
The UN warning came as Germany imposed border controls on Sunday, with police officials stopping cars and pedestrians near the border and checking passports, AFP news agency reported.
Germany's rail service Deutsche Bahn said train services with Austria were stopped until 03:00 GMT on Monday.
They have now restarted.
The move goes against the principle of the Schengen zone, which allows free movement between many European countries. However, the agreement does allow for temporary suspensions.
"The aim of these measures is to limit the current inflows to Germany and to return to orderly procedures when people enter the country," said German Interior Minister Thomas de Maiziere.
Germany says it is stretched to the limit by migrant arrivals, with 12,000 people arriving in Munich alone over the weekend. Germany expects 800,000 migrants to arrive this year.
The BBC's Damien McGuinness in Berlin says that Germany's move will put pressure on other European countries to do their bit and highlights just how much Germany is struggling to cope.
A steady stream of migrants is travelling from Greece, through Macedonia, Serbia and Hungary, to Austria and Germany.
The Czech Republic said on Sunday that it would also boost border controls with Austria.
In Hungary 5,809 migrants arrived on Sunday, a steep rise from the previous day's record of 4,330. The country is aiming to complete a four-metre-high (13ft) fence along the border with Serbia by Tuesday, when tougher measures, including arresting illegal immigrants, come into force.
To the south, Greek coastguards said on Sunday that at least 34 people, including 11 children, drowned when a boat carrying about 100 migrants capsized off the island of Farmakonisi in the Aegean Sea.