The reactors at the Yeonggwang plant about 205 miles southwest of Seoul account for about 5 percent of Korea's national power supply, the government said.
The parts, such as fuses and power switches, don't pose a risk of causing a radiation leak, the government said.
"We deeply regret the fact that such an incident took place but again I point out the fact that this has no direct link to the safety of nuclear reactors," Knowledge Economy Minister Hong Suk-woo said at a news conference Monday.
Hong said eight suppliers falsified 60 warranties for 234 different parts since 2003.
He said the government "will do its utmost to correct the problem at the earliest date possible."
Hong said that "comprehensive safety check-ups" were necessary at the two reactors, where the unqualified parts "were used extensively."
South Korea operates 23 nuclear reactors, providing for about 30 percent of its total electricity. It plans to build an additional 16 reactors by 2030, four of which are under construction.
Korea Hydro and Nuclear Power Co., the state-run operator of nuclear power plants, said nine malfunctions at South Korea's reactors have been reported since the beginning of the year.
This latest incident could further undermine confidence over the safety of South Korean reactors particularly amid increased scrutiny of nuclear power in the aftermath of Japan's Fukushima nuclear disaster.
Furthermore, the development could thwart South Korea's efforts to export nuclear power plants.
In 2009, a consortium led by Korea Electric Power won a contract valued at about $20.4 billion to build four nuclear reactors in the United Arab Emirates, marking the United Arab Emirates' entry into nuclear power. Construction for the first plant was approved in August.
Shortly after signing the Emirates deal, South Korea said in January 2010 that it aimed to achieve exports of 80 nuclear power reactors worth $400 billion by 2030.
"Nuclear power-related business will be the most profitable market after automobiles, semiconductors and shipbuilding," the Knowledge Economy Ministry had said, adding that South Korea would promote the industry "as a major export business."
On Monday, Hong stressed Korea's commitment to exporting nuclear power.
"The government plans to further increase its efforts to export nuclear reactors," he said, adding that Seoul "will quickly provide all necessary and accurate facts to prospective foreign buyers to make sure there is not a single shred of doubt left over the safety of the country's nuclear reactors."