Croatian Foreign Minister Vesna Pusic says Zagreb and Budapest have agreed to allow "vulnerable migrants" to cross the border into Hungary.
"Croatia and Hungary have agreed to co-operate and let groups of vulnerable migrants cross into Hungary," Pusic told AFP on Friday (local time).
While Pusic did not confirm who, or how many migrants would fall into the category, "vulnerable" has previously referred to women and children and the elderly.
But she insisted the agreement did not open up a new migrant "corridor" into the EU.
There has been no immediate confirmation of the agreement from the Hungarian side and earlier, its foreign minister denied any deal, accusing Croatia of encouraging migrants to break the law and illegally cross into Hungary.
"Croatian policemen claim that there is an agreement with the Hungarian interior ministry" to bus migrants towards Hungary, Peter Szijjarto told reporters on a visit to Belgrade.
"That is not true. We have never reached such an agreement. We would like to ask the Croatian government to stop spreading lies," he said.
Croatia has begun transporting hundreds of migrants to the Hungarian border, saying it can not cope with the flood of people on its territory.
Some 17,000 migrants have entered Croatia since Thursday morning, officials said.
Meanwhile, Croatian Prime Minister Zoran Milanovic discussed the crisis by telephone with German Chancellor Angela Merkel, the Government said in a statement.
"They agreed that the problem should be solved outside borders of the European Union," the statement said.