Hundreds of cars and buses were stuck on Slovenia's border with Croatia on Friday as tough checks on the EU's external frontiers came into force to stop suspected Islamist militants returning from Iraq and Syria.

The new directive coincided with the onset of the Easter break in Austria, Germany and Switzerland, leaving many frustrated holidaymakers on their way to southern Europe stranded in long traffic queues.

At the Obrezje crossing, people faced waiting times of at least two and a half hours to leave the passport-free Schengen area, according to the country's traffic information website.

Meanwhile buses crossing from Croatia -- which is part of the EU but not Schengen -- were stuck for around three hours or more.

Slovenia controls 670 kilometres (420 miles) of the external border with Croatia and was a key transit country along the so-called Balkan migrant trail until the route was shut in March last year.

"Until now systematic border controls were carried out only for non-EU citizens but now they also apply to EU citizens," Slovenian police chief Marjan Fank told journalists on Thursday.

"As a result there will be four times more work for border police and, consequently, longer waiting times," he added.

Croatian Prime Minister Andrej Plenkovic called on people to be "patient" while the new system was being implemented.

The EU said Thursday the systematic checks at the bloc's Schengen borders were designed to tackle "foreign fighters" returning from Iraq and Syria.