A police spokesman at the scene, Thilo Cablitz, said 1,500 officers had been called out to aid in clearing the Liebig 34 squat in the Friedrichshain neighbourhood.
An armoured car sat in front of the graffiti-festooned building and police kept onlookers at a distance.
Officers entered the building after residents refused to open the door for a court employee to deliver their eviction notice.
Some residents pumped their fists in the air as they were led down a ladder from an upper level by police, while others forced officers to carry them out.
On the distant peripheries, supporters of the residents threw fireworks and bottles at police. Mr Cablitz said other protests had been peaceful.
The building has been partially occupied for 30 years and subject to many court battles before the residents were finally ordered out of the apartments they had taken over.
As one of Berlin’s best-known squats, it was a symbol for the left-wing scene in the German capital, and police were braced for possible violence throughout the city.
