The southern city of Munich received another 3,600 on Saturday morning 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.
