But government officials said they do not expect importers to immediately move to get the beef out.
South Korean and US negotiators said over the weekend that they had reached a private-sector deal to restrict US beef exports to meat from cattle under 30 months old.
|Some 5,000 tonnes of US beef is waiting in South Korean storage for sale [AFP]
The agreement also forbids exports of parts that are thought to pose a higher risk of mad cow disease.
South Korean officials said the reworked pact would increase safety checks on US beef, but hours after it was announced a violent rally erupted in central Seoul with protesters smashing police buses blocking the way to the Blue House, the presidential residence.
Lee Myung-bak, who scored a landslide victory in last December's presidential election, has seen his popularity plummet to unprecedented lows after his government signed a deal in April to allow the import of US beef from cattle of all ages.
Public opposition to the deal escalated into nearly nightly protests against Lee's government, which wants to reform pension systems and privatise state-run firms.
Protesters have vowed to keep rallying until the original beef deal is scrapped or completely renegotiated.
Last week, Lee apologised for the original agreement, promised a fresh start for his four-month-old government and sacked most of his top aides.
On Tuesday, he ordered tough action against protesters who break the law.
US beef was banned from South Korea in 2003, after a single case of mad cow disease was discovered in an American herd.
South Korea had previously been the third-largest market for American beef.