Austrian officials say the checks, under a shared agreement with Germany, Hungary and Slovakia, have already uncovered more than 200 asylum seekers.
But authorities have begun allowing asylum seekers onto congested trains leaving Hungary as the pressure to implement a unified response to the issue grows.
Police in Austria have begun stopping every truck, van and car at the border in what authorities describe as an effort to capture people trying to smuggle asylum seekers.
The border checks have caused mass traffic jams, with lines stretching up to 30 kilometres long.
The raids have brought the arrests of at least five suspected smugglers.
Austria's Interior Minister Johanna Mikl-Leitner says the checks being undertaken along the Austrian border are not classic border controls.
"As of yesterday, we further increased the fight against people traffickers by carrying out intensive checks along the border and in the border area. These are not border checks but intensified search measures near the border." (German ...)
Hundreds of thousands of asylum seekers are trying to reach the European Union, fleeing violence and poverty in the Middle East and Africa.
At Budapest's main railway station, asylum seekers camp in the halls.
Until recently, they were unable to leave as a result of the border checks.
That restriction was lifted only because of the sheer number of people attempting to catch trains to other European countries.
Human Rights Watch's Lydia Gall was at the railway station and spoke to the BBC.
"It's just simply such a chaotic environment, and police are there, and people are literally fighting and jumping over each other to try and cut lines. These are the people that we have met. Until today, basically, people were unable to board these trains, even with tickets. And now that rumours have circulated that trains will accept people with tickets, more and more are lining up."
Last week, the discovery of 71 dead asylum seekers in a truck that had left Hungary brought the danger facing those fleeing their countries into sharp focus.
At a news conference, Germany's Chancellor Angela Merkel said the refugee crisis facing Europe is testing the core values of the European Union.
She says what she calls a "mood of racism" has overcome Europe and many are forgetting the desperation faced by those fleeing their home countries.
"We will apply the full force of the law against those who verbally abuse others, who attack other people, who set their shelters on fire or who want to use violence. We are against those who call for hate demonstrations. There is no tolerance for those who question the dignity of other people."
But Ms Merkel says simply changing attitudes to asylum seekers will not be enough to solve the crisis.
She insists a united approach from the European Union is needed to end people smuggling, as well as a solution that allows for fairer distribution of asylum seekers across the EU.
"We have a humanitarian responsibility. We need to establish registration centres and talk to African nations, talk to countries that are in civil war, and ensure there is a fair distribution of refugees across Europe, not like what is currently happening across Serbia, Macedonia and Hungary."
France's Prime Minister Manuel Valls agrees a fair distribution of asylum seekers in Europe is needed to prevent further deaths.
"We have to divide up equitably between European countries the reception of those who are eligible for asylum. Debates have been intense, but we have a framework. France, as Germany (does), supports it. Too many countries are refusing to take their share. It is against the European spirit. We cannot accept it."
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