Hyundai and its affiliate Kia have been ordered to recall around 240,000 cars after a whistleblower flagged safety defects.
The South Korean government issued its first ever compulsory vehicle recall over concerns that 12 different models were affected by the five flaws.
The transport ministry has also asked prosecutors to investigate whether there is any evidence of a cover-up.
Hyundai and Kia had earlier said the defects, which include issues with parking brake lights and fuel hoses, did not affect safety, and had rejected calls for a voluntary recall.
But they have now accepted the order, saying: "Safety is always Hyundai/Kia's number one priority and we make decisions on recalls or any other customer protection steps in compliance with regulators around the world and stringent internal procedures".