Japan's new centre-left government lifted a veil of secrecy Tuesday surrounding nuclear and military deals struck with the United States, formally abandoning decades of denials over the Cold War pacts.

A panel of historians Tuesday released a report commissioned by the six-month-old government on the "secret treaties," confirming previous information from whistleblowers, media leaks and declassified US documents.

The report officially confirmed that, from the 1960s Japan quietly allowed US warships to carry nuclear weapons across Japanese territory and, in the case of an emergency, to take them to US bases on the southern island of Okinawa.

The tacit agreements, previously denied, were reached despite Japan's pacifist stance and its official "non-nuclear principles" of not making, possessing or allowing on its soil atomic bombs, the panel found.

Foreign Minister Katsuya Okada told a news conference: "It is extremely regrettable that this problem for such a long time remained under cover, to the Japanese, even to parliamentary sessions, even after the end of the Cold War."

Okada said he could not rule out that US nuclear weapons had been brought into Japan but said he believed this had not happened since the United States in 1991 announced the withdrawal of tactical nuclear arms from its warships.

Japan, since its World War II defeat by the United States, which dropped nuclear bombs on Hiroshima and Nagasaki, has maintained a pacifist and anti-nuclear stance, but has relied on the superpower for nuclear deterrence.

The United States has some 47,000 troops stationed in Japan.

US-friendly Conservative parties ruled Japan for almost its entire post-war period but were ousted in landmark elections last August that brought to power the Democratic Party of Japan (DPJ) under Prime Minister Yukio Hatoyama.

Japan's new rulers have signalled a less subservient relationship with Washington, and more dovish foreign policy than previous governments, which had sent non-combat troops to support the US war in Iraq.

Hatoyama has angered Washington by saying his government may scrap a previous agreement to relocate a controversial US military base within Okinawa, which still hosts the bulk of the US troops stationed in Japan.

He stressed that it was important the report "would not affect future relations between Japan and the United States," Jiji Press reported.

Nuclear deterrence "is needed for the Asia-Pacific region as well as the Japan-US security treaty," he said, but stressed that pacifist Japan remained committed to its non-nuclear principles.

The panel of scholars found that the previous conservative governments of the Liberal Democratic Party (LDP) had for decades deceived the public.

Under another agreement, also long denied, Tokyo allowed US forces to launch military operations from Japan "as needed" without preliminary consultations in case of renewed war on the Korean peninsula, they said.

Former prime minister Eisaku Sato and then US president Richard Nixon also agreed in 1969, as part of talks on the 1972 return of Okinawa, that US forces could bring nuclear weapons on to the island in an emergency.

"For many years, the government repeatedly gave insincere explanations to its people, especially about the issue of nuclear-armed ship transits," said the historians led by Tokyo University's professor Shinichi Kitaoka.

Nagasaki mayor Tomihisa Taue immediately criticised the former conservative rules as "deceiving atom-bomb survivors who feel very strongly about the non-nuclear principles," Jiji Press reported.

After examining 4,423 files from Japanese foreign ministry and US embassy archives, the scholars highlighted 35 documents as proof of the existence of the clandestine agreements, with 331 items open to the public.

But they said many classified documents were missing, hinting that they may have been destroyed.