The Interior Ministry said that the decision was made to withdraw police from their headquarters in Port Said in light of the continued attacks on them and public property.
The ministry, in a statement, appealed to residents of the city to act to restore calm and stop the violence.
Earlier in Alexandria, dozens of striking officers and policemen shut down the Muharram Bek police station.
The protesters said they rejected recent decisions taken by the ministry, which forced them to tackle protesters.
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Army forces have been deployed in the city since violent protests hit the streets in January after 21 local football fans were sentenced to death over the riots, which left 74 people dead in 2012.
Army commander Brig Gen Mohamed Wassefy went to the security directorate and spoke with the crowd, including the families of the martyrs fallen lately in Port Said, the Ahram Online reported.