Hundreds of migrants are stranded outside a major railway station in the Hungarian capital, Budapest, after police sealed off the terminal to stop them travelling through the EU.
Government spokesman Zoltan Kovacs defended the closure, saying Hungary was trying to enforce EU law.
Thousands of people, many fleeing war and persecution, are trying to reach northern Europe to claim asylum.
EU states are engaged in a flurry of diplomatic activity to find a solution.
The crisis has highlighted the limitations of the EU’s system for coping with refugees, the BBC’s Chris Morris says.
Under an EU rule known as the Dublin Regulation, refugees should seek asylum in the first EU country they enter. But with countries such as Italy and Greece saying they cannot cope with the numbers, many have headed north.
Hungary had earlier appeared to abandon efforts to register migrants. However, Foreign Minister Peter Szijjarto told reporters on Tuesday that Hungary would now register all migrants and send those it considered to be economic migrants back to the state from which they entered the country.
