The panel said 61 members of its advisory committee stepped down and called for the resignation of Hyun Byung-Chul, who took office in July last year.
The National Human Rights Commission, founded in 2001, has important symbolic status in a country with a history of rights abuses under authoritarian army-backed regimes until the mid-1980s.
In a joint statement, the advisers denounced Hyun's alleged refusal to take action on sensitive political issues and claimed he had undermined the panel's independence.
"We have made a difficult decision to let people know about the seriousness of the current situation," Kim Deok-Jin, a Catholic rights group leader, told reporters.
The panel has 11 standing and non-standing commissioners nominated by parliament, the supreme court and the president, along with 160 advisers.
Two standing commissioners and one non-standing commissioner resigned earlier this month after criticising Hyun's leadership.
The panel has been split between liberal and conservative members over an investigation by state prosecutors into TV station MBC, which aired an investigative news programme into US beef, and over a ban on night rallies.
South Korea agreed in 2008 to lift a ban on most US beef imports. MBC's report on the alleged risk of mad cow disease fuelled weeks of mass street protests.
Prosecutors charged four MBC producers and a scriptwriter with defaming government officials by exaggerating the risk of the disease. In January a court rejected the charges.