Hundreds of refugees and migrants are still crossing the frontier, albeit at a slower pace than before the policy U-turn announced by Berlin on Sunday, police spokesman Rainer Scharf told AFP in the southern German town of Freilassing.
"The federal police department of Rosenheim has recorded around 1,000 people arriving since midnight," he said late Monday, referring to the Bavarian region over the border from the Austrian city of Salzburg.
Germany announced the new checks Sunday after authorities in the Bavarian state capital Munich said they were buckling under the waves of new arrivals.
Around 63,000 migrants came by rail to the main station in Munich since August 31, including 20,000 over each of the last two weekends.
Scharf confirmed that most came from the Middle East via Turkey, Greece, the Balkans, Hungary and Austria before arriving in Europe's top economy.
"Until now everyone was being shuttled to Munich," he said.
"Now we are carrying out a kind of pre-registration, taking people's names and so forth. Then they are being put on buses and can be distributed throughout Germany."
Chancellor Angela Merkel's spokesman said Monday that Germany was not slamming its doors to refugees but argued the new measures were needed to restore order to the asylum process.