Signs are up on the doors of the Thames St supermarket advising customers the premises was closed due to public safety risks, while a barrier was erected at the base of a ramp leading up to the main entrance.
A staff member approached by the Otago Daily Times declined to comment when asked why the supermarket was closed and said all questions needed to be directed to the company's head office.
Several people had reported on social media the supermarket was closed as a result of water entering the premises.
Electricity was also off inside the building.
According to the MetService, about 54mm of rain had fallen in Oamaru between 6am and 2pm.
Countdown is part of the Progressive Enterprises, a subsidiary of Woolworths Ltd.