Hungary has accused Croatia of committing "a major violation of international law" by trying to transport 1,000 people by train across its border.
Budapest described the train's unannounced arrival as a "major, major incident" - and alleged 40 police officers accompanying the migrants had to be disarmed and sent back.
Hungarian government spokesman Zoltan Kovacs said it showed "the Croatian system for handling migrants and refugees has collapsed, basically in one day".
"What we see today is a complete failure of the Croatian state to handle migration issues," he added.
"What is more, we see intentional participation in human smuggling, taking these migrants to the Hungarian border."
The refugees and migrants who were on the train are being transferred to a reception camp - and Hungary claims it has arrested the train driver.
According to local media, it has also called up military reservists to deal with the "mass migration situation".
It comes as a five-year-old girl has died and as many as 13 refugees are thought to be missing off the Greek island of Lesbos.
The Greek coastguard says 11 people were rescued from the sea between Lesbos and Turkey and one swam ashore in the early hours.
Hungary and Croatia
On the Hungarian border at Hegyeshalom, Sky News' Alex Crawford reported the country is now on a "virtual war footing".
As well as building fences, it has helicopters scouring the countryside and soldiers in armoured Humvee vehicles.
Its seizure of the train from Croatia is the latest development in a row that has left the fate of thousands of people uncertain.
Croatia's foreign minister, Vesna Pusic, said the countries had agreed "to provide a corridor" towards Austria, but Hungary's spokesman said that was a "lie".
More than 4,000 refugees and migrants were sent from Croatia to Hungary on Friday after officials said they could not cope with 17,000 who have arrived since Wednesday.
Reports suggest busloads of people were now being taken from Hungary to registration camps on the Austrian border.
Others are being taken towards Slovakia.
In other developments, Slovenian riot police used pepper spray overnight as they clashed with about 500 people trying to cross from Croatia and continue north.
Tensions
Tensions have been growing in Croatia as long lines of refugees wait to board trains and buses.
There were reports of clashes between desperate refugees from Afghanistan and Syria at the train station in Beli Manastir.
Elsewhere, some 2,000 people have gathered in Tovarnik waiting for transport.
Croatia's foreign minister Vesna Pusic says her country cannot handle the situation and says Europe must help out:
Temperatures are said to have been in the high 30s and 100 people had sought treatment for heat exhaustion and severe dehydration.
European Commission president Jean-Claude Juncker has called the Croatian prime minister to offer technical and logistical support - and was told the EU must strengthen its external borders.
EU leaders are to meet next Wednesday to try and agree a unified response to what has become the biggest movement of people in Europe since World War Two.
It comes as the Vatican said it had taken in a family of four from Syria, following a call by Pope Francis for every Church parish to house refugees.
Meanwhile, the Immigrant Council of Ireland is urging the Government to keep the Irish navy's presence in the Mediterranean under constant review.
Ireland is committed to having a vessel there until at least November.
It comes after the LE Niamh rescued a further 380 people off the Libyan coast yesterday.
Jerry O'Connor from the Immigrant Council says it could take years for the crisis to ease:
