Trains carrying hundreds of asylum seekers and migrants have started arriving in Vienna after Austrian authorities appeared to give up trying to apply European Union rules by filtering out those who had already claimed asylum in Hungary.

In the latest twist in a humanitarian and political crisis that is now testing the survival of both Europe's open-border regime and its asylum rules, Hungary allowed the people, many of them fleeing Syria's civil war, to cram into at least four trains leaving Budapest for Austria or Germany.

Many of the people arriving at Vienna railway station on Monday evening immediately raced to board trains heading on to Germany, as police looked on, preferring not to intervene, witnesses said.

A train also arrived in Munich from Budapest on Monday evening — German police said there were about 200 onboard.

In line with EU rules, an Austrian police spokesman said only those who had not already requested asylum in Hungary would be allowed through, but the sheer pressure of numbers finally prevailed.

The plight of these people highlights the huge challenge facing the European Union, which has eliminated border controls between 26 states of the "Schengen area" but requires new asylum seekers to apply in the first country they enter — in this case Hungary.

Most of the new arrivals have no intention of staying in Hungary, even those who register there, but aim to reach richer western European countries.

A Vienna police spokesman said people allowed into Austria could stay for two weeks while they decide whether to seek asylum there.

Those who did not would be returned to their last transit country.

Austrian authorities have stopped hundreds of people and arrested five traffickers as part of a clampdown along a main motorway from Hungary against the criminal gangs exploiting the human misery following last week's gruesome discovery of 71 dead people in an abandoned truck near the Hungarian border.

Schengen free movement principle under threat

A senior official at Austria's interior ministry, Konrad Kogler, denied on Monday that the clampdown, which includes increased checks on the eastern borders, amounted to a violation of the Schengen accord on free movement.

"These are not border controls," Mr Kogler said, noting that checks were taking place across Austria's territory as well.

"It is about ensuring that people are safe, that they are not dying, on the one hand, and about traffic security, on the other."

Migrants rush on the platform to make to their connecting German train after arriving in Vienna. ( AFP: Joe Klamar )

German chancellor Angela Merkel, whose country expects to receive 800,000 migrants and refugees this year, the most of any EU country, said the crisis could destroy the principle of free movement in Europe enshrined in the Schengen accord.

"If we don't succeed in fairly distributing refugees then of course the Schengen question will be on the agenda for many," she said at a news conference in Berlin.

"We stand before a huge national challenge. That will be a central challenge not only for days or months but for a long period of time."

Over the past three days, Hungarian police said they had caught 8,792 people crossing into the country, most of them from Serbia.

Hungary plans to tighten laws on migration this week and also plans to set up holding camps near the Serbian border.

The government left open the option of using the army to help police protect the borders if it received the necessary parliamentary approval.

The changes would also impose stronger penalties for the illegal crossing of borders and for damaging a 175-kilometre fence being built at the Serbian border, and would enable Hungary to expel people violating the new rules.

Reuters