Slovenia stopped all passenger traffic on the main railway line from Croatia, after finding 150 refugees on a Zurich-bound train. Croatian officials put the army on alert as thousands of people entered the country.
A group of 150 refugees arrived across the Croatian border late Thursday, Slovenian police officials said. It was the largest group to try to enter the country since the start of the refugee crisis, according to the police statistics.
"We will return them to Croatia in the shortest time possible," Anton Stubljar, from Novo Mesto police administration, told reporters.
Slovenia is likely to be the next stop step for the wave of refugees coming from Africa and the Middle East, with most newcomers seeking to reach wealthiest EU members further west and north.
Slovenian officials have stated, however, that they would not provide the migrants with a transit corridor, adding that such a move would be against EU asylum regulations.
Earlier on Thursday, Slovenian Prime Minister Miro Cerar said that the country was determined to stick to Schengen rules when dealing with the newcomers.
"We cannot let people who do not meet conditions to enter the European Union over the border," Cerar told the national TV station TV Slovenia.
Croatian President Kolinda Grabar Kitarevic asked on Thursday for the army to be ready to act if needed to protect the border from illegal immigrants, who are coming from the direction of Serbia.
Over 9,000 refugees have entered Croatia in less than 48 hours, according to the police. On Thursday, hundreds of migrants broke through police barriers, demanding to continue their journey towards Western Europe.
Faced with the influx, Zagreb temporarily closed seven border crossings with Serbia late Thursday, according to the DPA news agency. Police also banned traffic on roads leading to seven border crossings with Serbia, Reuters news agency reported.
Croatian Interior Minister Ranko Ostojic urged Serbian authorities to halt the migrants, and the migrants themselves not to come to Croatia.
"Don't come here anymore. Stay in refugee centers in Serbia and Macedonia and Greece," Ostojic said. "This is not the road to Europe. Buses can't take you there. It's a lie."
The right-wing government of Prime Minister Viktor Orban faced heavy international criticism over the incident, with UN General Secretary Ban Ki-moon calling the actions of the riot-police unacceptable. The European Union's migration commissioner, Dimitris Avramopoulos, also urged compassion for the migrants, adding that walls and violence were not the solution.
Tusk calls an emergency meeting
Despite the outcry, representatives of the Orban's government celebrated its sealed border on Thursday as a success.
"The assertive, uncompromising defense of the border has visibly held back human trafficking and forces them to change direction," said Janos Lazar, Orban's chief of staff. "That was the aim of the entire action."
"I find it bizarre and shocking that certain esteemed international figures have stood on the side of people who for hours were throwing stones and pieces of cement at the Hungarian police," Hungarian Foreign Minister Peter Szijjarto said.
"And I'd also like to make it very clear, no matter what criticism I receive, that we will never allow such aggressive people to enter Hungary," he added. "Not even for transit purposes."
European Union leaders are set to meet on Wednesday for an emergency summit on the refugee crisis, according to EU Council President Donald Tusk. The EU members are expected to discuss a proposed scheme to distribute 120,000 asylum seekers across the bloc.