Foreign Minister Katsuya Okada said that the investigation is in its final stages and that its findings will be announced in January. "We'll be unburdening ourselves of the insistence of past governments that a secret agreement did not exist," Okada said in a speech last weekend.

The pact violates a Japanese law that prohibits nuclear weapons from being made, possessed or stored on its territory. But disclosure of the 1960s-era agreement is hardly new. In general outline, its existence has been known for years because of declassified U.S. government documents.

Still, the Tokyo government's insistence on an official investigation of the matter has placed new strain on U.S.-Japanese relations.

"This is not the type of issue your closest ally forces you to confront publicly," said Ralph A. Cossa, president of the Center for Strategic and International Studies' Pacific Forum, a think tank in Honolulu. "At a minimum, it adds unnecessary friction to the alliance and makes U.S. ship visits, which are now routine, once again a source of contention and a rallying point for protest."

When Defense Secretary Robert M. Gates visited Japan last month, he reportedly told Japan's defense minister not to allow the investigation of the agreement to hurt bilateral relations or weaken U.S. nuclear deterrence. The U.S. government is treaty-bound to defend Japan in case of attack, and it has about 36,000 military personnel based here.

The traditionally close U.S.-Japan alliance has been knocked off balance in recent months by Prime Minister Yukio Hatoyama's insistence that Japan be more assertive in controlling the heavy footprint of U.S. military forces on its soil.

During President Obama's recent visit to Japan, he and Hatoyama agreed to create a working group of high-level officials from their countries to resolve a dispute over the location of the Futenma Marine air station in Okinawa. Noise and pollution from the base annoy local residents.

But the leaders have since disagreed over what the working group is supposed to do. Obama says it should focus only on implementing a three-year-old agreement to allow the air station to be relocated on Okinawa. Hatoyama says it must be able to do much more or else it is "meaningless." He has said he wants the air station moved off Okinawa or outside Japan.

The dispute over the air station has become a highly publicized symbol of Japan's new forcefulness in negotiations with its most important ally. It is also an early political test of the leadership ability of Hatoyama and his Democratic Party of Japan (DPJ).

To an even greater degree, Japan's probe of the secret nuclear pact with the United States is as much symbol as substance.

In part, that is because the pact is now moot: Both governments say U.S. vessels no longer bring nuclear weapons into Japan.

But disclosing its existence has a clear political upside for the DPJ, which won a crushing victory in recent lower-house parliamentary elections and is preparing for another election in the upper house in the summer.

Publicity about the pact is almost certain to embarrass the Liberal Democratic Party (LDP), which until this fall had ruled Japan as a virtual one-party state for nearly half a century and quietly decided in the 1960s to ignore the law when nuclear-armed U.S. ships entered Japanese ports.

The LDP's policy research council has said that full disclosure of diplomatic agreements "does not necessarily guarantee the protection of national interest."

Yet there may well be a political price to pay. There is a profound populist antipathy to nuclear weapons in Japan. The United States dropped atomic bombs on Hiroshima and Nagasaki in 1945, killing about 220,000 people.