The ex-Hyundai employee raised concern about defects which affected 12 different car models.
It is the first time the country's transport ministry has issued a compulsory vehicle recall.
Hyundai and Kia had refused to act voluntarily, saying any problems which did exist did not compromise safety.
Kia is an affiliate of Hyundai, and officials are asking the country's prosecutor to look for any evidence of a cover up at the carmakers.
The models affected include Hyundai's i30 hatchback, its Sonata midsize sedan, the luxury Genesis and Kia's Mohave as well as its Carnival minivan. These models and others were found to have issues with vacuum pipes, fuel hoses, parking brake light issues and several other faulty parts.
The planned recalls will add to the 1.5 million cars which Hyundai and Kia offered to fix last month in South Korea and the US over possible engine stalling.
In a statement Hyundai Motor said it accepted and respected the recall, but that there had been no "reported injuries or accidents from the cited issues".
"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."
When I met the whistleblower - by Karishma Vaswani, Asia Business Correspondent
Whistleblowing is rare in South Korea, and rarer still when the country's big family run conglomerates - or chaebols as they are known - are involved. The corporate culture and obeisance to the top bosses means that very few speak out of turn.
But they do exist. Last month I met Kim Gwang-ho, the 55-year-old man behind this specific Hyundai recall. He told me he'd decided to expose what was happening at the firm, because he couldn't - in good faith - allow passengers to travel in vehicles he knew to be faulty.
Mr Kim had worked at Hyundai for more than 25 years, and it was obvious to me that he cared deeply for the firm and was very proud of the work that he'd been involved in.
But he also pointed out that his decision to speak out was calculated. He was nearing retirement, and didn't have as much to lose as his younger colleagues.
A job in a chaebol is often seen as the only path to success in South Korea. And because getting one can be extremely competitive, many employees end up just toeing the line.
But Mr Kim's story, though, seems to have a positive ending. Just this month, Hyundai Motor dropped its lawsuit against him, reinstated him to his old job, and reimbursed him for the lost years of employment.
It was what South Korea's Anti-Corruption and Civil Rights Commission ruled years ago, but it took Hyundai until now, perhaps amidst the changing political environment, to heed it.
(Source : BBC)
