Croatia has closed seven of eight border crossings with Serbia

11,000 people entered Croatia in 48 hours after Hungary's crackdown on migrants

Migrants are prevented from boarding a bus by riot police, at the border between Serbia and Croatia, in Tovarnik, Croatia (AP)

Croatia has closed seven of eight road border crossings with Serbia because of an influx of over 11,000 migrants who evaded police to enter the country.

The closures – the day after Hungary fenced off its border with Serbia – is the latest desperate attempt by European governments to stem the flow of people hoping to reach countries such as Germany in the border-free Schengen area.

Officials in Zagreb said they were left with no choice after huge numbers of people broke though police lines, trekked through fields and entered rural villages, following the crackdown by Hungary, which has drawn international condemnation.

Others trying to enter Slovenia by train from Croatia were intercepted by border police, with officials stopping all rail traffic on the main line between the countries.

Between Croatia and Serbia, only the main Bajakovo crossing, on the highway between Belgrade and Zagreb, appeared to be open to traffic on Friday.

Migrants have been streaming into EU member Croatia for two days, with their path into Hungary blocked by a metal fence, as police fired tear-gas and water cannon on groups of angry migrants who threw stones. Budapest has threatened to imprison anyone trying to illegally enter the country.

There were desperate scenes at a railway station on Croatia's eastern frontier with Serbia, where thousands were left stranded overnight under open skies.

The EU has called an emergency summit next week to overcome disarray in the 28-nation bloc.

Croatian Interior Minister Ranko Ostojic warned on Thursday that Croatia would close its border with Serbia if the flow of migrants continued at the same rate, saying his country was full to capacity.

Serbia's border with Croatia has become the latest flashpoint in Europe's refugee crisis (Getty/EPA)

Late on Thursday, police announced they had banned all traffic at seven border crossings. "The measure is valid until further notice," police said in a statement. Serbia's main highway north into Hungary is already closed by Hungarian riot police on the border.

READ MORE:

It remained unclear whether or how police would stop migrants, many of them refugees from Syria, from streaming through fields across the border away from official crossings, though their path across much of the frontier is made more difficult by the River Danub.

Serbia warned its neighbours against shutting down the main arteries between them.

There, Slovenian police halted a train carrying some 150 migrants at Dobova train station on Slovenia's side of the border and said they would be sent back. A Reuters TV crew said some tried to leave the train but were stopped by police. Some refused water in protest.

Slovenia – the eastern extreme of the Schengen area - has also introduced border controls, as Ljubljana announced on Thursday that its frontier with Hungary would be closed for at least 10 days.

UN secretary general Ban Ki-moon condemned the Hungarian border police on Thursday, describing their actions as "not acceptable".

Additional reporting by Reuters