The vast majority of the over 86,000 refugees who crossed into Slovenia so far came through Rigonce on foot after being dropped off at a Croatian train stop, creating massive problems for Slovenian law enforcement.

This afternoon, however, a train carrying some 1,070 refugees from Opatovac in east Croatia crossed into Slovenia for the first time.

It took the refugees to Dobova, the main international rail crossing on the Slovenian side of the border, Interior Ministry State Secretary Boštjan Šefic said.

A processing centre for refugees has already been set up there. Once the formalities are completed, the refugees will be taken by train to reception centres inland.

If things go according to plan the intention is to to make Dobova the main entry point for refugees.

"We are keeping a close eye on how things are working. We will analyse [the system] and see whether any upgrades are needed," Šefic said, describing it as "a big step forward" in improving the situation in the area.

The switch to the new system is also a sign of improving cooperation between Slovenia and Croatia, which Šefic described as "significantly better".

Both countries have also set up round-the-clock contact points in accordance with an agreement reached Sunday at a Balkan migration summit hosted by EU Commission President Jean-Claude Juncker on Sunday.

Šentilj as the main exit point from Slovenia has also been under heavy pressure, with several thousand refugees converging there every day awaiting entry into Austria.

The arriving refugees exit the train there a kilometre or two before the accommodation centre, but arrangements are now being made to allow the train to take them further, just a few metres from the camp.

"A makeshift platform will have to be built, but I do not see this as a major problem," Šefic said.

By midday today over 5,800 refugees had entered Slovenia, bringing the total to almost 86,500.