Hundreds of migrants are in a standoff with police for a second night outside a Budapest railway station.
Earlier, scuffles broke out between the two sides as frustration among migrants boiled over outside Keleti station.
Many of the migrants have tickets and are insisting they be allowed to travel on to Germany and other countries, but Hungary says it is enforcing EU rules.
Meanwhile, Germany, Italy and France have called for "fair distribution" of refugees throughout the EU.
In a joint declaration, the countries' foreign ministers also called for Europe's asylum laws to be revised, the Italian foreign ministry said in a statement (in Italian).
With tens of thousands of migrants from the Middle East and Africa on the move through Europe, the EU's member states are struggling to agree a common policy for dealing with the crisis.
Italy and Greece have complained that they are overwhelmed by the numbers arriving on their shores. And while countries such as Germany are prepared to accept large numbers of asylum seekers, others, such as the UK, are not.
The BBC's Chris Morris in Brussels says the European Commission, the executive of the EU, is trying to draw up a list of safe countries of origin that failed asylum applicants can be sent back to.
And an EC spokeswoman has now said it is preparing proposals for a mechanism to automatically redistribute a proportion of those seeking asylum among EU states.
The migrants camped overnight at Keleti station had been prevented from boarding trains on Tuesday.
They had bought tickets after Hungary appeared to abandon efforts on Monday to register migrants, allowing huge numbers to board trains to Vienna and southern Germany.
Hundreds of migrants again protested on Wednesday, chanting "Freedom, freedom" and waving train tickets.
Journalists at the scene said tensions were high with migrants involved in a stand-off with riot police.
A confrontation also broke out an another railway station in Budapest where a group of migrants occupied a platform after refusing to board a train sending them to a reception centre in the eastern city of Debrecen.
Police quoted by Hungarian TV said the "illegal immigrants" held their children aloft and demanded they be allowed to proceed freely to Germany.
Prime Minister Viktor Orban is due to meet EU chiefs on Thursday to discuss Hungary's handling of the crisis.
Under an EU rule known as the Dublin Regulation, refugees should seek asylum in the first EU country they enter.
But this has proved hard to uphold, with border countries such as Hungary, Italy and Greece saying they cannot cope with the numbers. All three are members of the borderless Schengen Area.
In another development, spot checks on the border between Italy and Austria have been intensified following a request from Germany, Italian officials said.
The northern province of Bolzano said the German state of Bavaria had asked for "logistical support".
Bavaria, particularly the city of Munich, has seen record numbers of migrants arriving from the south. Austria is also performing spot checks on its border with Hungary.
The German government has already said it will allow Syrians arriving from other EU states to apply for asylum. But on Tuesday, a spokesman said the Dublin Regulation had not been suspended.
German Chancellor Angela Merkel has called for asylum seekers to be distributed more equally across the EU.
But on Wednesday, UK Prime Minister David Cameron said that taking "more and more" refugees was not the answer.
Greece saw the arrival of 23,000 migrants last week alone, said the EU's border control agency Frontex - an increase of 50% on the previous week.
Many arrive on the island of Lesbos, where, according to the Kathimerini newspaper, 17,500 migrants were registered in the last week.
Some 4,200 migrants were brought from Lesbos to the port of Pireaus, near Athens, early on Wednesday.
Greece's government says it lacks the resources to look after so many arrivals, but aid groups say the authorities should be doing more.
The number of migrants entering Europe has reached record levels, with 107,500 arriving in July alone.
Germany expects to take in 800,000 migrants this year - four times last year's total.
The risks for those travelling through Europe were highlighted last week by the deaths of 71 people found in a lorry that had travelled to Austria from Budapest.
EU interior and justice ministers will meet in Brussels on 14 September to address the crisis.