The deputy police chief of Austria's Burgenland state, Christian Stella, was quoted by APA as saying that Hungary had not given enough warning about the size of the influx.
On the other hand, Hungary accused Croatia of breaking the rules by failing to register the migrants - some told the BBC that Hungary had not registered them either. The migrants had been sent from Croatia into Hungary, which in turn shipped them on to Austria, BBC reported.
The Croatian Interior Minsitry reproted on Saturday evening that 28 buses with migrants had departed from Tovarnik, the eastern Craotian town on the border weith Serbia, towards Hungary. An additional 1,000 were transported by train.
Although Croatia has closed seven out of the eight border crossings with Serbia, migrants are being entering Croatia from Serbia in significant numbers.
Also, a Croatian-Slovenian border crossing has been closed, according to a report from the Croatian auto club (HAK), which reported disruptions in traffic.
To date, over 2,000 refugees have entered Slovenia from Croatia on their way to western European and Scandinavian countries.
Slovenian Foreign Minister Karl Erjavec told the national television on Saturday that the country's capacity was to accommodate a maximum 9,000 migrants, and Ljubljana was in permanent contact with Austria and Germany regarding this issues.
The Slovenian media have reported that a majority of those refugees are Syrians, Afghans and Iraqis and that 90 % of them say that they want to go to Germany or Scandinavian countries.
While visiting the border areas of Brezice and Novo Mesto, Slovenian Prime Minister Miro Cerar said on Saturday evening that all incoming migrants had been identified and registered in Slovenia in accordance with the European rules. He commended the conduct of the local police.
Cerar confirmed that he had several telephone conversations with his Croatian counterpart Zoran Milanovic.
"In these circumstances, Slovenia must show solidarity, and it is also important to continue implementing the (relevant) measures when there are so many foreign persons in the country," Cerar said.
Croatia has seen over 20,000 migrants entering from Serbia since Wednesday "and, after initially welcoming them, (Croatia) said it was unable to cope and moved them on," the BBC said.