However, the German interior ministry said a daily upper limit on border crossings had not yet been agreed by the two countries.
“We would like to have a more orderly procedure,” said a spokeswoman for Germany’s interior ministry, with the new measures intended to reduce long waiting times to cross the border.
The number of refugees crossing the Bavarian border remains high, and by midday on Saturday more than 1,000 migrants had either crossed into Germany or were waiting to enter at entry points at Wegscheid and Simbach am Inn.
Tensions grew between Germany and Austria earlier this week when German Interior Minister Thomas de Maizière accused Austria on Wednesday of transporting asylum seekers to its 500-mile-long border at night without any warning.
But the Austrian authorities hit back, with a police spokesman dismissing such accusations as “a joke” that Bavaria was unable to process the new arrivals, given that 11,000 people a day were entering Austria just at the Spielfeld crossing from Slovenia.
Several hundred right wing supporters rallied at that border crossing yesterday (Saturday), marching on the refugee camp with banners reading “No Way” or “You will not make Europe your home”. A smaller group held a counter-protest, holding signs proclaiming “Refugees Welcome.”
The move comes as Angela Merkel, the German chancellor was holding crisis talks this weekend over the migrant influx with Horst Seehofer, head of the CSU and prime minister of Bavaria, and Sigmar Gabriel, the vice-chancellor and head of coalition partner the Social Democrats.
Germany expects to receive at least 800,000 asylum applications by the end of this year, although some estimates have put the figure higher at 1 million.
Last Wednesday, more than 8,000 migrants arrived in Bavaria, according to German police, while last week, authorities in Passau said they had been overwhelmed by a new influx of around 15,000 people arriving from Austria.
Several hundred had to spend a night out in the cold on the Austrian side of the border before reaching Germany after Austrian authorities said they had run out of beds for them.