The attacks come amid concerns that North Korea may mount cyberattacks against industrial and social targets after accusations by the United States that Pyongyang was responsible for a devastating hacking assault on Sony Pictures.
South Korea is still technically at war with the North.
South Koreas energy ministry said it was confident that its nuclear plants could block any infiltration by cyber attackers that could compromise the safety of the reactors.
"Its our judgment that the control system itself is designed in such a way and there is no risk whatsoever," Chung Yang-ho, deputy energy minister, told Reuters by phone.
An official at Korea Hydro and Nuclear Power Co Ltd (KHNP), the nuclear plant operator that is part of state-run Korea Electric Power Corp, told Reuters that the hacking appeared to be the handiwork of "elements who want to cause social unrest".
"It is 100 percent impossible that a hacker can stop nuclear power plants by attacking them because the control monitoring system is totally independent and closed," the official said.
Neither Chung nor the KHNP official made any mention of North Korea.
They also said they could not verify messages posted by a Twitter user claiming responsibility for the attacks and demanding the shutdown of three aging nuclear reactors by Thursday.
The user who was described in the posting as chairman of an anti-nuclear group based in Hawaii said more documents from the nuclear operator will be posted if the reactors are not closed.
Seoul prosecutors are conducting a criminal probe into the leak of data from KHNP, including blueprints of some nuclear reactors, electricity flow charges and radiation exposure estimates.
They have traced the IP used for a blog carrying the stolen documents to an online user in a southern city who has denied knowledge about the postings and claimed his user ID has been stolen.