The Shingori 1 in Busan, 280 miles south of Seoul, was shut down after a problem was detected involving the control rod that governs the rate of fission in the reactor, Yonhap News Agency reports.
About 2 hours later, the second reactor -- at Younggwang Nuclear Power Plant in South Jeolla province, about 220 miles south of Seoul -- was shut down due to low water levels.
Officials at state-run Korea Hydro and Nuclear Power said that neither reactor was in danger of releasing radiation, Yonhap reports.
South Korea relies on nuclear energy for about 30 percent of its electricity needs. The country has 21 active nuclear reactors.
Despite safety concerns about nuclear power in the wake of Japan's Fukushima nuclear power disaster in March 2011, Seoul has stood firm on its commitment to increase that share to 40 percent by 2040.
Tuesday's problem follows similar incidents at two other reactors, one in July and another in August, in which reactors were shut down due to rod control system problems, South Korea's The Hankyoreh newspaper reports.
Tuesday was the first time that the Shingori was shut down due to a malfunction since it began commercial operation in February 2011.
But the Woleseong No. 1 reactor shut down in August, has had 52 malfunctions since it went online in 1983, says the Korea Federation of Environmental Movements.
The Hankyoreh reports that 105 accidents and technical problems have occurred at South Korean nuclear power plants from 2000 and last month.
KHNP says the recent problems all had been assigned an International Atomic Energy Agency risk level of zero because the control rod issues wouldn't immediately lead to an accident involving the release of radiation.
But if the problems occurred in tandem with a natural disaster such as the earthquake that struck Fukushima, The Hankyoreh's report says, a rod control failure could lead to a devastating accident.
Until now, KHNP or Korea's Nuclear Safety and Security Commission hasn't ordered special investigations related to the shutdowns.
"If you consider that we added another two reactors this year, there hasn't been a huge increase in power plant shutdowns, nor is there any commonality in the places and causes of the technical problems," Yoo Kook-hee, the NSSC's safety policy bureau chief, was quoted as saying by The Hankyoreh.
Still, Yoo said independent examinations were under way to see if the problems might be associated with some shared vulnerability.
Yang-Lee Won-young, head of the Korea Federation of Environmental Movement's bureau for post-nuclear energy, warned against the reactors being put back into operation too soon.
"KHNP and the NSSC need to take this opportunity to uncover the root cause and allay the public's fears," Yang-Lee said.