Some Balkan countries are screening refugees at borders, allowing those who can prove they are fleeing conflict in the Middle East and Afghanistan to travel on, but turning back some from Africa and Asia, witnesses said.
The overnight move, which prioritised refugees from Syria, Afghanistan, and Iraq, left hundreds of people stranded at border crossings on Thursday.
"It is not acceptable that people who want to seek asylum are being segregated by nationalities. The right to ask for asylum is universal and cannot be connected to certain nationalities," said Stephane Moissaing, MSF head of mission in Serbia.
"We’re extremely worried about the latest developments and fear that people will be stranded without any assistance, shelter and food, just as winter sets in. We're seeing people who are desperate because they don't have any information on where to go or what they should do next."
In Serbia, from Wednesday evening, Serbian border police stopped people crossing from Macedonia if they did not have papers stating that they were Syrians, Afghans or Iraqis.
In the Serbian border town of Presevo, MSF witnesses said they saw women from Somalia and two from Afghanistan who did not have papers - one of whom was pregnant - camped outside the registration centre after being sent away.
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On Serbia's frontier with European Union-member Croatia, about 400 people were denied access to a train and were halted by Croatian police as they tried to cross the border through fields.
"Macedonia, Serbia and Croatia are now stopping all who cannot identify themselves as refugees coming from these three countries affected by violence," said Melita Sunjic, a spokeswoman for the UN refugee agency UNHCR.
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Other refugees were stuck in no-man's land between Macedonia and Greece, where Macedonia closed off access to all refugees regardless of nationality until a deal could be reached with Greece on how to filter them, Reuters reported.
Slovenian police announced on Wednesday that they would return those considered to be "clearly economic migrants and not refugees" to Croatia if they had entered the country from there, the STA news agency reported. Croatian Interior Minister Ranko Ostojic, however, called the plan "unacceptable" on Thursday.
"The Balkan route is only open for refugees from Syria, Afghanistan and Iraq. Others are treated as illegal immigrants and sent back," said 'Are You Syrious', a group aimed at keeping refugees informed, in a recent Facebook post.
'Many are fleeing terrorism'
The move comes amid fears prompted by the Paris attacks that among the hundreds of thousands of refugees trying to escape war and persecution could be people planning attacks in Europe.
Rights groups have warned against conflating refugees with violent attackers.
"Many [refugees] are fleeing extremism and terrorism - from the very people associated with the Paris attacks," said UNHCR spokesperson Melissa Fleming. "A world that welcomes Syrians can help defeat extremism. But a world that rejects Syrians, and especially Muslim refugees, will just feed into their propaganda."
Earlier in the week, far right groups across Europe seized on the reports, calling for borders to be sealed.
Unprecedented numbers of refugees have travelled to Europe in 2015. By mid November, Human Rights Watch said, more than 800,000 had reached Italy and Greece, with smaller numbers arriving in Spain and Malta.
According to the UNHCR, 84 percent have come from Syria, Afghanistan, Eritrea, Somalia, and Iraq.
Elsewhere on Thursday, Norway's political parties agreed that the country will tighten its asylum policy to dissuade refugees from coming, AFP reported.
Since the beginning of the year, 29,000 people have sought asylum in the country of 5.2 million, including 2,500 people in the past week alone.
The ruling parties, the Conservatives and the anti-immigration populist Progress Party, reached an agreement with their centrist allies and the Labour opposition, giving them a broad parliamentary majority to limit the number of refugees coming to the Scandinavian country.
Under the deal, the government will reduce asylum seekers' social benefits, putting them on a par with levels in neighbouring Nordic countries to make Norway less attractive, and speed up the processing of some cases and the expulsion of rejected asylum seekers.
It will also limit access to permanent residency, and make it harder to qualify for family reunifications.
With reporting by Anealla Safdar: @anealla
Source: Al Jazeera and agencies