The US is dispatching a team of experts to Japan to oversee US shipments of beef, in an effort to persuade Tokyo not to reimpose a total ban on imports.
The size of the Japanese market makes a ban a very costly problem
Japan said the ban would resume after outlawed spinal material was found in a 390kg batch of meat from New York.
It came only a month after a two-year embargo on US beef - imposed over fears of BSE (mad cow disease) - was lifted.
US Agriculture Secretary Mike Johanns admitted an "unacceptable failure", but denied any threat to public health.
He said US exports to Japan would from now on face stricter controls, and that US inspectors in Japan would scrutinise American shipments at Japanese ports.
BSE was found in US cattle at the end of 2003, prompting Japan to impose the import ban.
Previously, Japan was the most lucrative export market for US beef producers, and the Bush administration lobbied intensively for the ban to be dropped.
Last month, the Japanese government agreed to allow imports of products from cattle less than 21 months old, as long as parts thought to have a higher risk of carrying BSE, like spinal cords, vertebrae, brains and bone marrow, were removed.
Eating beef from infected cattle can cause a fatal human brain disorder, Creutzfeldt-Jakob disease.
US beef accounted for a significant part of the Japanese market, and its absence has forced some dishes to be taken off restaurant menus.
In response to the latest incident, fast-food chain Yoshinoya said on Saturday it was postponing the planned return of a popular beef dish.
"There appear to be large problems with compliance, which we feel is extremely regrettable," said a spokesman.
A Japanese government spokesman said Tokyo would lodge a protest with US Deputy Secretary of State Robert Zoellick, who was due to arrive in Tokyo on Saturday on a previously arranged visit.
The loss of its most profitable market has already hit US producers and the price of cattle futures fell on the Chicago Mercantile Exchange.