Two South Korean banks, Shinhan Bank and Nonghyup, and three TV stations KBS, MBS and YTN, all reported that their networks had suddenly shut down on Wednesday afternoon.
An official close to the investigation told the BBC it was believed a "malicious" code was to blame for the system failure.
He said investigators were trying to identify and analyse the virus.
Initially, South Korea's Communications Commission suspected a cyber attack.
However, experts concluded it was not a denial-of-service attack, of the kind South Korea has experienced in the past.
North Korea has been blamed for several breaches over the past few years.