Sydney police say an officer appears to have accidentally shot himself this morning while trying to holster his gun.

Several officers were chasing after a man who was allegedly trying to break into a store in Chatswood in the city's north at about 5 am.

Acting superintendent Peter Yeomans says the 31-year-old officer suffered a gun shot wound in the leg while trying to make the arrest.

"At this stage, it's a critical incident investigation, so I can't go too far into it," he said.

"But it appears at this stage that the officer has tried to re-holster his weapon."

The officer is being treated in hospital and is said to be in good spirits. He will have surgery later today.

The male break-in suspect was arrested shortly after the shooting.

A critical incident investigation is underway.