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They received a report of a person with a gunshot injury at 7.30am today.
The incident is understood to have taken place near St Patrick's Cathedral in Wyndham St.
Police said the man was found in a vehicle and was taken to hospital in a moderate condition.
"Police are currently at the scene making inquiries into this incident."
St John said three ambulance teams, including a rapid response unit, attended.
A patient was taken to Auckland City Hospital in a moderate condition, a spokesperson said.
A local business owner told The New Zealand Herald that the church caretaker said a person had been found injured outside the building.
She said she did not believe there had been a shooting at the site.
"Somebody was shot and then he was left at the back of the church."
The woman said she did not hear any gunshots this morning, but that she had seen police in the area from about 7am.
"It's scary. It's like what you seen in a movie."