Vilsack agreed Thursday with this Japanese counterpart, Hirotaka Akamatsu, to launch talks on beef, which he called a "significant area of disagreement" in trade relations.
Washington wants to start "as soon as possible," Vilsack said. He said President Barack Obama's negotiating team will include trade representatives and officials from the Department of Agriculture.
"We are not there yet. We are still apart," Vilsack said in a speech at the Foreign Correspondents' Club of Japan. "But I believe we have developed a relationship that I believe over time hopefully will result in us figuring out what we've been unable to figure out up to this point."
Japan banned U.S. beef imports in December 2003 after the first case of mad cow disease was found in the United States. Shipments resumed in January 2006, but under strict restrictions.
U.S. beef shipped to Japan must come from cattle age 20 months and younger, considered less at risk for the disease. American exporters must also remove spinal columns, brain tissue and other materials from shipments bound for Japan.
Mad cow disease, or bovine spongiform encephalopathy, is a degenerative nerve disease. In humans, eating meat products contaminated with the illness is linked to variant Creutzfeldt-Jakob disease, a rare and fatal malady.
Vilsack said American beef is safe but said trade policy under Obama better reflects local characteristics and conditions.
"So when I came here to talk to the minister yesterday, I wanted to make sure he understood that I understood the need for the United States to be sensitive to the concerns and anxieties of the Japanese consumer," he said.
The U.S. has had no BSE cases in the last three years, and only three over the last two decades, Vilsack said. He said the government has also improved safety inspections and training over the past year.
Trade rules should be based on science and in line with international standards, Vilsack said.
Japan has discovered some three dozen cases of mad cow and tests all cows headed for the slaughterhouse - a measure Washington considers excessive. The U.S. Department of Agriculture tests about 1 percent of cows for the disease. Japanese inspectors have found banned cow parts in shipments, a violation of the trade accord that has added to Japan's worries.
Talks on the issue had been stalled for more than two years. Washington in the past had demanded Tokyo scrap all age restrictions. But the Japanese farm minister told reporters it now appears willing to accept a more gradual easing in order to rekindle trade.
The renewed effort is part of Obama's National Export Initiative, which seeks to double U.S. exports in five years to help create 2 million jobs. Launched in February, the government-wide strategy calls for a more aggressive fight against trade barriers.
Vilsack estimates that every $1 billion in trade-related agricultural activity generates 9,000 jobs.
Japan was the largest consumer of U.S. beef until the late-2003 ban. It now ranks third behind Mexico and Canada, according to the National Cattleman's Beef Association. The U.S. shipped 81,345 metric tons of beef and beef products to Japan last year, about a quarter of 2003 levels. Revenue is down 65 percent.