(CNN) -- San Francisco police are saying a man they thought was fatally shot by officers actually killed himself.
Police earlier said Kenneth Harding was shot by an officer Saturday while trying to run away.
But on Thursday, authorities said they found evidence that proved something different.
"We believe that the fatal wound on Mr. Harding was self-inflicted," said police Cmdr. Mike Biel.
Biel revealed the new theory at a news conference Thursday at the city's medical examiner's office.
Kenneth Harding died Saturday after a confrontation with undercover officers who were doing a fare check on passengers on the city's Muni bus transit system.
Police say when he was approached by the officer who wanted to see his ticket, Harding ran and police pursued him. During the chase, a gunbattle started and Harding was fatally wounded,
Initially, authorities believed that San Francisco police shot and killed Harding during the confrontation in the city' Bayview-Hunters Point neighborhood.
The shooting triggered angry protests by some community members who challenged the police version of what happened.
The medical examiner said new evidence reveals a different story.
"The bullet which was recovered from his head is not consistent with the service ammunition used by the San Francisco Police Department," Chief Medical Examiner Amy Hart told reporters.
She demonstrated her point with a photo of the bullet removed from Harding's head.
It was a .380-caliber and San Francisco Police are armed with .40-caliber ammunition, Hart said.
Medical examiner's staff also found a second, unfired cartridge (.380-caliber) in Harding's right jacket pocket. Harding was also wounded in the leg by a round apparently fired by pursuing officers, authorities said.
"Based upon evidence known at this time including: officer and witness statements that Harding shot at the police officers, Shot Spotter data, video tape evidence that depicts a firearm at the scene that was subsequently taken and the location of gunshot residue on Harding's right hand, it appears that Mr. Harding's head wound was self-inflicted. It is unknown if Harding's injury was intentional or accidental."
When the shooting occurred, a crowd had gathered challenging officers, police said in a statement released at the news conference.
At one point, a bystander recorded cell phone video of the situation, including a handgun that was laying on the ground near Harding.
The Police Department believes that the weapon used by Harding is still outstanding along with a cell phone and bullet casings removed from the scene.
Authorities are offering a $1,000 reward for the return of the .380-caliber firearm picked up from the scene.
Harding was listed as "a person of interest" by Seattle Police who were investigating the shooting death of a young woman in that city a few weeks ago, CNN affiliate KGO reported.