A German police spokesman warned on September 13 that Munich, the main point of entry to Germany, is at the limit of its capacity to welcome refugees entering the country through Austria.
German police said that a total of 12,200 migrants arrived in Munich on September 12.
Around 700 people had arrived at the main station on the morning of September 13, according to federal police spokesman Simon Hegewald.
Three special trains are due to move the migrants to other parts of the country.
Meanwhile, the flow of migrants into Hungary hit another record on September 12 after more than 4,000 people walked across the border with Serbia.
Hungary is in the process of completing a four-meter high fence on its border with Serbia and as of September 15 will enact new rules that criminalize border crossings and speed up decisions about asylum requests.
Based on reporting by AP, AFP, and BBC