Austria strengthened coronavirus controls on its border with Slovenia on the weekend, causing traffic chaos and angering Slovenian police until they relented on Sunday.

From Saturday until noon on Sunday, Austria stopped every car entering from Slovenia to record personal data from all passengers to help track infections after a spike in cases, Austrian police said.

Long stretches of cars - many driven by German and Dutch tourists returning from summer holidays - were backed up from the Karawanks and Loibl tunnels, busy crossing points between northern and southern Europe.

A Slovenian police spokesman told the APA news agency that authorities on their side of the border had not been informed of the change.

"We were in no way prepared for such slow and restrictive work methods on the part of the Austrian authorities," the spokesman said Sunday.

"With such a system, as it was applied by the Austrian side yesterday and last night, the situation is not humane."

Slovenian police said they took a child suffering from heatstroke in one of the cars to hospital.

There were 12 kilometres of traffic jams at the Karawanks entrance on Sunday, until local authorities on the Austrian side of the border eased the measures, unblocking traffic, which returned to normal on Sunday afternoon.

Vienna said it imposed the border controls after a third of the holidaymakers returning to Austria who tested positive for coronavirus over the last month were coming from Croatia, a popular beach destination south of Slovenia.

Croatia's foreign ministry called for a solution to be found to shorten the "worryingly long" wait time at the Austrian border, the state-run HRT radio reported.