Police said up to four people who were in the clinic at the time escaped soon after the stand-off began and were not physically harmed.
It is not yet known for certain whether the man fired shots at police or staff.
The man is yet to be formally identified, but is believed by police to be a local south coast resident.
He does not have an extensive criminal record and is known to police largely through previous medical and psychological episodes that required intervention.
Assistant Commissioner Peter Cotter said the man, 34, was known to the medical centre and staff.
“During conversations with the doctor the man has become extremely agitated and spoke to many alarming things.
“During that conversation, and unprovoked, he produced a firearm.”
Staff contacted police who established a perimeter around the building and started negotiations with the man.
Up to four people escaped the surgery while negotiations were under way, leaving the gunman by himself.
“During this time police continued their conversations with the gunman through the open door and through the walls and the windows,” Cotter said.
After nearly two hours the man emerged from the clinic and continued to engage with officers before brandishing the firearm at them, police said.
“The police at the time were holding a ballistics shield [which] was dropped during this initial confrontation and the police retreated,” Cotter said.
“The man picked up the shield, further brandished the gun, raising it in the air and raising it at police.
“A number of shots were fired by police in the direction of the man. He was hit multiple times.”
Multiple officers on the scene fired shots at the man, according to police.
A little while later the man was pronounced dead, despite the efforts of paramedics to save him.
“The next of kin of this man have been informed and obviously it is a tragic time and a tragic event for all his family and all of his friends,” Cotter said.
“Police respond to protect life. They responded today in absolute good faith.”
A critical incident team from the police homicide squad is investigating the circumstances leading to the death which will also be subject to an independent review.