The first batch of refugees, mostly Syrians, coming by a special train from Hungary via Austria arrived in Germany on Saturday.
According to German police, they initially expected at least 400 refugees on the special train, Xinhua news agency reported.
However, only 250 refugees have arrived so far.
The special train arrived at Munich's central station in the afternoon. Another train of German railway company Deutsche Bahn was already waiting at another platform.
After disembarking from the special train, refugees were directed by police to the waiting train, which is said to ride to a first reception centre, 3 km west of the central station.
Police said that another special train as well as 12 regular passenger trains carrying hundreds of refugees are expected to arrive in Munich later in the day.
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Hungary had decided on Friday night to bring refugees stuck at Budapest by bus to the Austrian border. Austria and Germany then declared their willingness to accept them.
Altogether, up to 10,000 refugees are expected to arrive in Germany.