Japan and the US have maintained a security alliance since World War II
Japan has confirmed the existence of a secret Cold War deal allowing the transit of nuclear-armed US vessels through its ports.
The move by a government-appointed panel ends decades of official denial - although the existence of the pact was an open secret.
The government said that the move was aimed at increasing transparency.
But it comes at an unsettled time for the US-Japan relationship, amid a row over US military bases in Okinawa.
The secret pact is controversial because after World War II and the atomic bombings of Hiroshima and Nagasaki, Japan adopted the three "non-nuclear principles" - not making or possessing nuclear weapons, nor allowing them on to its soil.
The secret deal was sealed in the 1960s between US and Japanese diplomats, who agreed that the transit of nuclear arms through ports did not constitute the introduction of weapons into Japan, and so did not require prior consultation on the US side.
''By leaving the issue ambiguous, (US) ships carrying nuclear weapons could stop at Japanese ports without prior consultation, while Japan, as its official stance, could deny such a development. But neither side would make a protest,'' Kyodo news agency quoted the panel's report as saying.
Declassified US documents had already confirmed the deal.
A cable from US ambassador Edwin Reischauer detailing a breakfast meeting in April 1963 with Foreign Minister Masayoshi Ohira explained how the two discussed the pact and achieved "full mutual understanding" on the transit issue.
But the deal has been denied by successive Japanese governments, because of fears of public anger.
The probe into the deal was ordered by the new Democratic Party government, which ousted the ruling Liberal Democratic Party last year after more than five decades in power.
The panel also confirmed the existence of deals relating to the use of US military bases in Okinawa in the case of an emergency on the Korean peninsula and the cost of the 1972 reversion of Okinawa from US to Japanese control.
Foreign Minister Katsuya Okada told a press conference it was "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".
Japan and the US have maintained a security alliance since the end of World War II, and the US has almost 50,000 troops stationed at bases across Japan.
But Japan's new government has indicated it wants what it calls a more equal relationship with the US and has said it wants to reduce the US military presence on the island of Okinawa.
A row over plans to relocate the Futenma airbase in Okinawa has chilled ties between the two long-time allies.