The group, camped out on the city's central Rindermarkt square, had originally been demanding the right to asylum in Germany but signalled they would be prepared to accept residence permits issued on humanitarian grounds instead.
When this was not offered to them during negotiations, the group said they would continue the protest. Many said they were prepared to die.
Doctors had previously warned that many of the protesters were in a critical condition.
According to the Süddeutsche Zeitung newspaper, authorities had wanted to avoid moving protesters, who were camped out legally. However city mayor Chirtsian Ude said “protecting lives” was his “utmost priority.”
Forty-four of the protesters were admitted to 12 hospitals, according to city spokesman Stefan Hauf.