The cause of the fire is thought to have been a gas explosion.
Some 50 families had moved into the building after the Federal Police Force, which had been using it, vacated some years ago.
Despite an earlier message posted onto the department's official Twitter account suggesting that one person had been spotted calling for help on the building's upper floors, the spokesman says the department does not expect any deaths or injuries. A firefighter told Globo TV that they expected to find victims but did not know how many.
The governor said it was legally hard to force people to evacuate the old and decaying buildings.
In a July 2017, story on the residences, The Associated Press reported that around 350 families were living in the former police headquarters.
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The fire began overnight and spread rapidly, turning the building into an inferno.
Brazilian President Michel Temer visited the ruins early Tuesday morning, but rushed away after victims began throwing rocks and debris at his auto. "I had to come, despite these protests, because I was in Sao Paulo, and it would have looked bad if I didn't", he told journalists.
The city and state governments have for years sought to remove squatters in a bid to clean up and revitalize the center of Latin America's most populous city. The government estimates that almost 4000 families are living in vacant buildings downtown.
In this photo released by Sao Paulo Fire Department, a building on fire is seen in Sao Paulo, Brazil, Tuesday, May 1, 2018. "Others are less established and more precarious".