TOKYO » They were Tokyo's worst-kept diplomatic secrets: clandestine Cold War era agreements with Washington that obligated Japan to shoulder the costs of U.S. bases and allow nuclear-armed U.S. ships to sail into Japanese ports.

For decades, Japanese leaders have gone to great lengths to deny the pacts' existence, despite mounting proof to the contrary from the testimony of former diplomats and declassified documents in the United States. The most sensational instance came in 1972, when a reporter who unearthed evidence of one of the treaties was arrested on charges of obtaining state secrets, reportedly by means of an adulterous affair.

Now, the so-called secret treaties are causing problems again, this time in how Japan is handling its suddenly rocky relationship with the United States.

The new government in Tokyo, whose election last summer ended a half-century of nearly unbroken control by the Liberal Democrats, wants to expose the treaties as a showcase of its determination to sweep aside the nation's secretive, bureaucrat-dominated postwar order. Last fall, the foreign minister appointed a team of scholars to scour Japanese diplomatic archives for evidence of the treaties. Its findings are due later this month.

The problem is that the inquiry is coming at a delicate moment in Japan's ties with its longtime patron, the United States. The government of Prime Minister Yukio Hatoyama of Japan and the administration of President Barack Obama are already divided over the relocation of a U.S. air base on the island of Okinawa. By exposing some of the less savory aspects of Japan's military reliance on the United States, the investigation has drawn criticism, particularly from conservatives in both nations, as an effort by the left-leaning Hatoyama government to pull away from Washington.

However, those involved in the investigation in Japan, both within and outside the government, insist that it is not about challenging the American alliance. In interviews, the current central figures in the case—including the foreign minister, Katsuya Okada; a retired Japanese diplomat who helped reveal the pacts' existence; and the reporter who got the original story, Takichi Nishiyama, now 79 and still fighting to restore his reputation—described the investigation as an effort to expose agreements from the 1960s and early 1970s that were too old to have an impact on current diplomatic relations.

Okada and the others emphasized that the existence of the treaties had already been made public in the United States. Some also said that the Japanese investigation was drawing attention only because it was so unusual for this nation to reveal its past after years of obfuscation under the long-governing Liberal Democrats. They said the investigation was a highly symbolic gesture by the new government to make Japan's stunted democracy more forthcoming and accountable to its own people.

“;The prime minister and I cannot just stand before parliament and deny the secret treaties, as has been done until now,”; Okada said. “;We are just doing what the United States has already done.”;

Diplomatic experts agree that exposing the treaties will have little or no direct effect on the alliance, partly because the United States announced in the early 1990s that it was no longer carrying nuclear weapons on most of its warships.

But the investigation could have unintended consequences if it uncorks long-suppressed public debate on a point that Tokyo has, until now, purposefully left vague: whether Japan, which officially bans nuclear weapons from its territory, can continue to rely on the United States' nuclear umbrella, which may require it to allow carrying such weapons on U.S. ships and planes in a time of crisis.

This could lead to calls to remove the U.S. bases, rewrite Japan's pacifist constitution to allow a full-fledged military or even develop the country's own nuclear deterrent, political observers said.

“;This is the biggest contradiction of the postwar period,”; said Masaaki Gabe, a professor of international relations at University of the Ryukyus in Okinawa Prefecture. “;The Democratic Party could be opening a Pandora's box of public debate.”;

According to experts, there were four known secret pacts, made when the two countries revised their security pact in 1960 or during negotiations for the return of the southern islands of Okinawa to Japan in 1972. One of the first to expose them was Nishiyama, then a rising reporter at the newspaper Mainichi Shimbun.

His revelations provoked a battle pitting the public's right to know against government demands for secrecy that many here likened to the Pentagon Papers in the United States. But unlike the Pentagon Papers case, the journalist lost in Japan.

Public attention quickly turned to his arrest and the details of his affair with a Foreign Ministry worker, which he admitted took place.

However, he says the tabloid aspects of the case were highlighted by prosecutors to divert public attention from discussion of the secret pacts themselves. Japan's Supreme Court found Nishiyama guilty of obtaining state secrets in 1978, and he has been filing lawsuits ever since, seeking an official apology and the disclosure of documents related to the treaties.

“;Why do the Japanese people only learn about their own government from documents disclosed in the United States?”; he said. “;This is crazy.”;

Nishiyama and a handful of civic groups seeking evidence of the pacts got a boost in 2000, when the United States began declassifying documents related to the secret agreements. An unexpected breakthrough came four years ago, when a diplomat who had testified at Nishiyama's trial that the pacts did not exist—Bunroku Yoshino, one of the negotiators of Okinawa's return to Japan—came forward three decades later to admit that he had lied.

“;After dozens of years have passed, you cannot keep distorting history,”; said Yoshino, now 92.

Okada, the foreign minister, said he was aware of the criticism that the investigation was anti-American, which he called a misunderstanding. He said exposing the truth would actually strengthen the alliance by righting a past wrong that had led many Japanese to doubt the sincerity of their own government and the United States.

“;Telling the facts to the people is extremely important for democracy,”; he said, adding that the change in Japan's government “;is a great chance”; to do so.