The co-CEO of a South Korean company that owns the country's biggest mobile messenger app stepped down on Wednesday following a massive service outage that left more than 50 million without access to its widely used services for days.

Kakao's flagship messaging app KakaoTalk is installed on around 90 percent of phones in the country and its heavily used services include maps, online payments, ride-hailing, streaming and gaming.

The outage started on Saturday after a blaze broke out at SK C&C's building in Pangyo, south of Seoul, which houses the company's server.

Most of its services were restored as of Wednesday morning, the company said.

"As a CEO of Kakao, I feel miserable and take to heart my grave responsibility for the incident," Namkoong Whon said in a news conference, as he announced his resignation.

"We bow our heads and sincerely apologise to all users who have experienced inconvenience due to the service failure."

Upon Namkoong's departure, Hong Eun-taek is now the firm's sole CEO.

Hong acknowledged the company was not prepared for a "complete shutdown of an entire data centre".

"KakaoTalk has now become a public service as the majority of people use it. We could not fulfill our responsibilities accordingly," he said.

Kakao was founded in 2010 and its messenger service has about 53 million users globally, according to a filing in August.

The malfunction is a blow for hyper-wired South Korea, which aims to stay at the forefront of technological change.

South Korean President Yoon Suk-yeol has called for an investigation into the cause of the damage and plans to prevent similar incidents in the future.

Kakao said it will "fully cooperate" with the investigation and plans to invest 460 billion won (US$322 million) to open its own data centre by next year, and start building an additional facility in 2024. (AFP)