"We would like to have a more orderly procedure," a spokeswoman for the interior ministry told the AFP news agency, saying Germany had reached agreement on the new policy with the Austrian government.
"The rule will go into effect immediately," she added.
Tempers flared between Berlin and Vienna this week when Germany's Interior Minister Thomas de Maiziere on Wednesday hit out at Austria for sending asylum seekers to its 800-kilometre-long (500-mile-long) border without any warning.
Authorities in the southern German state of Bavaria, already struggling to cope with the record numbers, complained that the lack of coordination was leaving them scrambling to find resources to assist the new arrivals.
But Austrian authorities hit back, with a police spokesman calling it "a joke" that Bavaria was unable to process the new arrivals.