While declassified US documents have already confirmed such 1960s agreements, Tuesday's revelation broke with decades of official denials.
The investigation by a government-mandated panel is part of Prime Minister Yukio Hatoyama's campaign to rein in the power of bureaucrats and make his government, which was elected to power last year, more open than that of the long-ruling conservatives, who repeatedly denied the existence of such pacts.
“It's regrettable that such facts were not disclosed to the public for such a long time, even after the end of the Cold War era,” Foreign Minister Katsuya Okada told a news conference, adding that the investigation was meant to restore public trust in Japan's diplomacy.
The panel examined documents surrounding four pacts, including Tokyo's tacit permission that US nuclear-armed warships could make calls at Japanese ports - a violation of Japan's so-called three non-nuclear principles not to make, own or allow the entry of atomic weapons.
There is strong aversion to nuclear weapons in Japan, the only country to suffer atomic bombings - in Hiroshima and Nagasaki at the end of World War II.
Speculation about the existence of such secret agreements have been swirling in Japan for years so the panel's findings most likely will simply confirm public suspicions rather than shock or anger people. Some are also aware of US documents about these matters.
Analysts welcomed the move as a positive step toward more transparency in the Japanese government but said it probably won't revive the sagging popularity of Hatoyama's government or affect US-Japan ties, which have grown strained recently because of a dispute about relocating a key Marine base on the southern island of Okinawa.
“It's a good thing for Japanese democracy, given that the previous governments have been telling blunt lies to the public,” said Koichi Nakano, a political science professor at Sophia University in Tokyo.
“But I don't think it's going to have a short-term impact on the government's popularity,” he said. “A lot of people look at this as something that belongs to history.” Under a security alliance with the US, some 47,000 American troops are stationed in Japan, and the US protects the country under its nuclear umbrella.
Okada said it was possible that before 1991, when the US stopped carrying battle-ready nuclear weapons, American warships might have had nuclear weapons as they entered Japanese waters or entered Japanese ports.
Reacting to the six-member panel's findings, summarized in a 108-page report, Hatoyama said there would be no changes to Japan's non-nuclear policy.
The panel, led by University of Tokyo professor Shinichi Kitaoka, said that while documents showed that Washington and Tokyo appeared to have differing interpretations about allowing nuclear-armed ships into Japanese waters, it was likely that Tokyo and Washington shared an unspoken understanding permitting them to make port calls in Japan without consent.
The experts also acknowledged that Tokyo and Washington had secret agreements allowing the US to use military bases in Japan without prior consent in case of emergency on the Korean Peninsula during the Korean War.
The panel said it could not find specific evidence showing a secret pact allowing the US to bring nuclear weapons into Okinawa after the 1972 reversion of the island to Japan. But it acknowledged that there was a vague secret agreement over Japan's cost burdens for Okinawa's 1972 reversion to Japan.
