Reports said the probe is a blow to South Korean President Lee Myung-bak. Lee, who won the presidency last year in a landslide, now has an approval rating below 20 percent.
The opposition Democratic Party demanded the probe in exchange for ending its boycott of parliament. The party had boycotted the National Assembly in protest against the beef deal.
The ruling Grand National Party agreed earlier this week to accept a probe and parliament is to be formally opened Friday.
The opposition has reportedly claimed that the beef deal, made in April and amended last month to limit it to beef from cattle younger than 30 months, is flawed because it could expose the country to mad cow disease.
American beef went on sale earlier this month, but is still not widely available because supermarket chains and restaurants are reluctant to sell or serve it because of the protests.
Source: Associated Press