In Washington, White House spokesman Gordon Johndroe said Bush assured Lee that the U.S. government "is cooperating closely with the South Korean government and ready to support American cattle exporters as they reach a mutually acceptable solution with Korean importers on the beef trade."
Lee initiated the call a day after South Koreans staged the biggest-yet rally against the beef import deal, which they say fails to protect the country from mad cow disease by allowing meat from cattle of any age.
Police said 65,000 people took part in the protest, in which dozens of demonstrators and riot police were injured.
South Koreans have been taking to the streets for weeks to criticize Lee over the deal, claiming he ignored their concerns about mad cow disease, behaved arrogantly and gave in to U.S. demands.
Protesters have urged the government to scrap the agreement and negotiate a better one.
The government has ruled out any formal renegotiation.
Lee said Friday that demanding a renegotiation would spark a trade dispute with Washington that could affect South Korea's export-driven economy, especially its key auto and semiconductor industries.
He also said that the government would seek other ways to keep beef from older cattle from entering the country, and that the United States is "actively cooperating" to find a solution.
The beef dispute has turned into a political crisis for Lee, who took office just three months ago on a wave of popularity for promising to revitalize the economy.
But his approval ratings have nose-dived since the beef pact. A poll published in a major newspaper days ago put his public support at less than 20 percent.
Lee was forced to cancel a traditional opening speech at the new National Assembly this past week because of an opposition boycott of the legislature.
All of his top aides offered to resign on Friday. In South Korea, senior officials sometimes offer to step down during times of crisis to deflect or diminish criticism of an embattled leader.
It was not clear whether Lee would accept the resignations.
U.S. beef has been banned from South Korea for most of the past four and a half years since the first case of mad cow disease in the U.S. was discovered in late 2003. Two subsequent cases were found.
Scientists believe the disease spreads when farmers feed cattle recycled meat and bones from infected animals. The U.S. banned recycled feeds in 1997.
In humans, eating meat products contaminated with the illness is linked to variant Creutzfeldt-Jakob disease, a rare and fatal malady blamed for the deaths of over 150 people worldwide, mostly in Britain.