Some 40,000 migrants could arrive in Germany over the next two days, officials say – double the number who entered the country last weekend.
Most are expected to arrive in the southern city of Munich but there are concerns about how the region will cope with another large influx.
Around 4,000 troops are being deployed in Germany for logistical support.
Germany has become an attractive destination for Syrian refugees since it waived EU rules.
The government announced in August that it would deal with Syrian asylum applications regardless of where the migrants first arrived in the EU. Up until then, people had to claim asylum with the first EU country they reached.
Tens of thousands of mainly Syrian migrants have been making their way from Turkey, through the Balkans and Hungary to reach Austria, Germany and Sweden.
Migrants have continued to arrive in Macedonia from Greece. More buses were reported to be making their way towards the Hungarian border this weekend.
Munich Mayor Dieter Reiter, has appealed urgently for other German regions to do more to process and accommodate the new arrivals.
He described as “scandalous” the failure of other regions to provide more accommodation, according to state broadcaster ARD.
Reports suggest the government is considering new temporary powers to take control of unoccupied rental property to accommodate migrants.
A large processing hub is planned for northern Germany, on Lueneburg Heath. Trains would take migrants there directly from Austria.