Police said the incident, which occurred at about 11pm on Monday, off Portobello Rd near Glenfalloch, was called in by the owner of the car last night.
There were no injuries.
Concerned members of the public reported the car again this morning, which prompted police and fire services to attend the scene at 7.30am to ensure the car was the same one as had been reported last night.
Firefighters have secured the car in the Otago Harbour until it can be towed out of the water later today.