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.
The mayor of Munich, 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 in Lower Saxony. Trains would take migrants there directly from Austria.
Ten of thousands of people are due to participate in a “day of action” with dozens of events taking place in several countries.
A handful of rival anti-migrant protests are also due to take place.
In Hamburg, a demonstration by the far-right was banned earlier this week but the main railway station was closed on Saturday after left-wing demonstrators attacked a train believed to be carrying neo-Nazis.
Several thousand people joined a peaceful demonstration in the city centre in support of tolerance and diversity.
Image copyright EPA Image caption The tolerance rally in Hamburg was organised in opposition to the far-right demonstration, which was banned Image copyright AP Image caption An Afghan migrant child sleeps in Munich station
The crisis has exposed deep divisions within the European Union. The European Commission announced plans for obligatory quotas to share out 120,000 additional asylum seekers among 25 member countries.
The Czech Republic, Hungary, Poland and Slovakia oppose being forced to take in new arrivals.
Hungarian Prime Minister Viktor Orban has called on the European Union to give Syria’s neighbours €3bn (£2.2bn; $3.4bn) in financial aid to help those displaced by the civil war.
Mr Orban said supporting Turkey, Lebanon and Jordan with such a package would end the mass migration to Europe.
In an interview with Germany’s Bild newspaper (in German), Mr Orban said the €3bn fund could be raised by every EU country paying an extra 1% into the budget – or by a general reduction of EU spending by 1%.
Hungary has struggled to cope with some 150,000 migrants that have crossed its borders so far this year and from next week, people who enter the country illegally will be arrested.
There have been tensions between authorities and migrants across Hungary, as thousands try to pass through en route from Greece to countries in northern and western Europe.
In the past few days, aid workers have spoken of “abysmal” conditions for refugees at a camp in Roszke on the Hungarian-Serbian border.
Hungary has insisted it is trying to fulfil its obligations as an EU member and register all new arrivals.