A spokesman for the company said the recall was a precautionary measure and that BMW was unaware of accidents and injuries caused by the possible defect.
Around 89,000 vehicles in the U.S. and 22,000 vehicles in Germany are affected by the move.
BMW could not immediately say how much the recall would cost.
According to the U.S. National Highway Traffic Safety Administration's website, BMW is recalling certain Mini Cooper, Cooper S, Clubman, Cooper JCW, Clubman, Countryman and Convertible models.
The electric auxiliary water pump that cools the turbocharger has an electronic circuit board that can malfunction and overheat, the NHTSA's website said. The circuit board may smoulder, which could result in a vehicle fire, the website further said, adding that BMW will notify owners and dealers will replace the water pump free of charge.
The safety recall is expected to begin during February 2012, the NHTSA's website said.
(Reporting By Irene Preisinger and Edward Taylor; Editing by Steve Orlofsky)