Germany said on Friday that refugees would only be able to enter the country at five points along its border with Austria in an attempt to control a mass influx of refugees who have been crossing into the southern German state of Bavaria daily.
"We would like to have a more orderly procedure," a spokeswoman for the interior ministry told AFP adding that Germany had reached agreement with the Austrian government on the 800km (500 mile) border.
"The rule will go into effect immediately," she said.
According to the agreement, 50 refugees an hour could cross into the state at the five agreed point, a senior Bavarian politician said.
Earlier this week, anger between Berlin and Vienna climbed up when German Interior Minister Thomas de Maiziere on Wednesday accused Austria of transporting refugees to Germany's 900-kilometre-long (500-mile-long) border at night without informing them.
Bavaria has already been struggling to deal with the record numbers that reached the state. Bavarian authorities complained that the lack of coordination with Austria was hindering efforts to find resources to help new arrivals.
German Federal Police Spokesman Heinrich Onstein said that all attempts were being carried out to prevent the refugees from having to sleep outdoors.
Onstein said the problem was that "we do not know how many people will arrive, and at which border post."
However, an Austrian police spokesman dismissed the accusations calling it “a joke.” He said that Austria was receiving 11,000 refugees a day at the Spielfeld entering from Slovenia, and Bavaria could not process the new arrivals.
Germany expects at least 800,000 refugees this year as some estimates indicate that it may be as high as 1.5 million.
German police stated that more than 8,000 refugees arrived in Bavaria last Wednesday.
Authorities in Bavarian town of Passau, which is a major transit point for refugees, said last weekend that the town had been overrun by a new flow of some 15,000 people who came from Austria.
Before reaching Germany, the refugees spent a night outside on the Austrian side of the border as there was no bed left for them, said Austrian authorities.
Many refugees continue to make their way via Greece to get asylum in Germany as they faces harsh winter conditions.
On Friday, 21 people died after two boats carrying refugees from Turkey to Greece sank overnight in the eastern Aegean Sea while they were trying to reach European Union countries, which are the latest deadly incidents.
Greek officials said that 18 people died and 138 were rescued near the island of Kalymnos as another separate incident early on Friday left three dead and six rescued off the island of Rhodes.
Tens of thousands of refugees from conflict-hit states in the Middle East and Africa have been trying to flee to Europe in recent months.
According to new figures by the UNHCR, 107,500 people crossed the Mediterranean Sea to reach Europe only in the last month, some of them pay large sums of money to smugglers to get them through borders illegally.
UNCHR figures show that at least 2,636 people have died as they attempt to enter Europe in 2015.