Authorities in Bavaria have complained a lack of co-ordination with Austria is hampering efforts to aid new arrivals.
Many others continue to make their way via Greece, in freezing temperatures, hoping to get asylum in Germany.
Meanwhile, more than 20 migrants - many of them children - have drowned in more boat sinkings in Greek waters while they were trying to reach European Union countries via Turkey.
Greek officials said 19 people had died and 138 were rescued near the island of Kalymnos.
Three others died off Rhodes and three were missing. Six were rescued there.
And the Spanish coastguard called off the search for 35 migrants missing at sea the day after their boat was shipwrecked en route from Morocco.
Fifteen migrants were rescued alive from the vessel and the bodies of four others were found.
New influx
A spokeswoman for Germany`s interior ministry told AFP news agency that the new rules on entry points would go into effect immediately.
"We would like to have a more orderly procedure," she said.
A senior Bavarian politician said that under the agreement, 50 migrants an hour could cross into the state at the five agreed points.
More about:
