The demonstrators want an April agreement to resume imports of US beef rescinded and renegotiated.
The deal has sparked public outrage amid widespread perceptions, fanned in part by sensational media reports, that it exposes the country to a higher risk of mad cow disease.
The government says a full renegotiation of the beef deal would hurt the country's international credibility.
The protesters are also denouncing other policies of Lee Myung-bak, the president, including his plan to privatise state corporations.
Lee, a conservative who took office in late February, apologised to the nation twice over his handling of the beef issue and replaced all his top advisers.
Earlier on Saturday, about 400 conservatives held a rally calling for an end to the anti-government protests.
"Stop illegal, violent candlelight demonstrations!" they shouted.
They accused their opponents of using fear of mad cow disease to undermine the president.