The argument erupted after French industry minister Luc Chatel told French radio that Renault would relocate part of its production from Slovenia to a plant at Flins, near Paris, creating 400 jobs there.
A Renault spokeswoman said the company intended to increase production both in Slovenia and France and the shift was intended to meet a shortfall in capacity at its Slovenian plant.
It denied the move was linked to a pledge to keep jobs in France in exchange for state aid.
But EU competition commission Neelie Kroes told the BBC she was highly surprised and was seeking urgent clarification from the French authorities.
Ms Kroes said she had received a pledge from Mr Chatel just a few weeks ago that an $8bn state bail-out for carmakers would not be linked to moving jobs to France, our correspondent reports.