"At least 10,000 people" were expected at the train station in the Bavarian capital today, said Eva Hinglein, spokesperson for the Upper Bavaria district.
Between midnight and 10:30 am, authorities counted 3,600 migrants.
Munich Mayor Dieter Reiter has said that he is "very concerned with the developments".
"We no longer know what to do with refugees," Reiter said
So far this year, 450,000 refugees have arrived in Germany, including 37,000 in the first eight days of September, Vice Chancellor Sigmar Gabriel told parliament on Thursday.
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The cheers have been replaced by a sort of grim routine: as soon as migrants get off the train, police shepherd them to welcome centres to begin their registration.
Still the attitude among the arrivals remains one of gratitude.
"The problem isn't them (the Germans), it's just that's there are too many people", a 22-year-old Syrian refugee Adel told AFP.
Despite this surge, "they welcome us anyway, they welcome us with everything, food, everything."
But Munich is quickly reaching capacity.
"We think that 5,000 people tonight will not know where to go," to spend the night, said a local official, Christoph Hillenbrand.
He said many of the migrants will have to make do with mats on the ground.
To help accommodate them, the city with the help of the army has installed beds on its fair grounds.
German media has reported the possibility of a large welcome centre to open in the north, hopefully taking some of the pressure off of southern cities like Munich. But the government has not confirmed it.