It happened around 9:19 a.m. Wednesday at the building in Tioga-Nicetown.
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Police say the 23-year-old suspect was trying to communicate with an officer through protective glass, but the officer couldn't hear the man - who was wearing a mask.
The officer then opened the locked side door to the office, and that's when the suspect lunged with the screwdriver, officials say.
There was a physical struggle involving the three officers inside.
"They attempted to disarm this individual while he was swinging the screwdriver in their direction - this was all within about 30 seconds. Right around that time one of the officers that were in the operations room fired at least one shot at this individual, striking him in the torso," said Philadelphia police spokesman Sgt. Eric Gripp.
One of those officers, described as a 32-year-old woman with seven years on the force, fired her weapon.
The suspect was shot in the torso. He was taken to the hospital where he was listed in critical but stable condition.
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A male officer sustained a head injury during the scuffle. Officials believe he suffered that injury during a fall and do not believe he was stabbed with the screwdriver.
The officer who was injured was taken to the hospital to be treated.
A second officer sustained upper-body injuries to his arm and elbow.
The female officer was not physically injured.
"This is yet another example of the kind of violence that not just our officers of the street encounter, but some of our community members are exposed to on a daily basis," Commissioner Danielle Outlaw said during a Wednesday afternoon gun violence briefing.
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As with all officer-involved shootings, the discharging officer will be placed on administrative duty pending the outcome of an investigation, Outlaw said.
She sent a letter to her officers to offer support and access to mental health services.
"Our officers will not be deterred, and we will not be intimidated, and we will not rest in our mission to keep the public safe from those who attempt to cause harm to others," she said.
Part of this use of force investigation will include if the officers were wearing active body-worn cameras and if they had access to Tasers.
There are not any surveillance cameras inside the 39th District building.