The Japanese government of the day, headed by prime minister Eisaku Sato, was desperate to take back control of the prefecture but was aware that officially permitting the US military to place nuclear weapons on Japanese soil was unacceptable to the people of a nation that was the first to be the target of an atomic bomb.

To this day, Tokyo refuses to confirm or deny that any agreement existed – written or unwritten.

The Japanese foreign ministry was contacted for comment on the discovery of the document but has not replied.

The US, however, confirmed rumours of the agreement as far back as 1996, although the full text of the accord remains classified.

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On December 11, 1967, just three years before the secret deal was sealed, Sato addressed the Japanese House of Representatives and stated: “My responsibility is to achieve and maintain safety in Japan under the Three Non-Nuclear Principles of not possessing, not producing and not permitting the introduction of nuclear weapons, in line with Japan’s Peace Constitution.”

The document discovered in Nixon’s Presidential Library in Yorba Linda is dated November 24, 1969, three days after the US president and Sato agreed to the return of Okinawa to Japanese control. It had been overlooked by previous researchers, Gabe said, because it was erroneously filed among papers related to another issue the two leaders had discussed – textile exports.

Addressed to Henry Kissinger, the president’s national security adviser, the memorandum suggests Kissinger emphasised that the trust Nixon had built up with a number of foreign leaders was “paying off”, and that Nixon was achieving diplomatic outcomes that would have been beyond president John F. Kennedy, his immediate predecessor.

Nixon also instructs Kissinger to have “a very private meeting” with a number of senior US politicians to “give them some reassurance with regard to our use of the Okinawa bases without violating our agreement with Sato with regard to secrecy”.

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“Perhaps the best way you can get this across is to simply say we have some private understandings that we will deny if anything should ever be said about them but that they are very satisfactory as far as General Wheeler is concerned,” the memorandum states.

General Earle Wheeler served as chief of staff for the US army during Nixon’s administration, and apparently had reservations about returning Okinawa to Japanese control if the US did not retain the right to keep nuclear weapons in the prefecture.

“Nixon said he was ‘satisfied’ because most people in Congress thought that if a deal was made then the US would lose the right to freely station nuclear weapons in Okinawa,” Gabe said.

“The Japanese side asked the US to respect their non-nuclear principles, which would have meant they would have to withdraw any nuclear weapons if they were directly asked if any were in Okinawa,” he said.

The two sides got around this problem by Japan asking the US to comply with its position, and the US, which has a policy of not divulging sensitive military information, declining to state whether it had deployed nuclear weapons on Okinawa. That, Gabe said, provided Tokyo with plausible deniability.

“So they reached an agreement that, on the surface, kept Japan satisfied but also allowed the US – which was deeply involved in the war in Vietnam – to keep their weapons in Okinawa,” he said. “It was easy to deny for both sides.”

Ivan Tselichtchev, a professor at Niigata University of Management, said the Japanese government’s policy of “ask no questions, get told no lies” could prove problematic if Gabe’s discovery attracted widespread media attention in Japan. To date, the story has been reported in the Mainichi newspaper and issued by the Kyodo News wire agency, but there appears to be little follow-up.

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“If this is actively raised by the mass media, then it could send shock waves through bilateral relations,” he said. “It may very well have a negative effect on public opinion and perceptions of US defence policy and US-Japan relations as a whole.

“President [Donald] Trump has set a new direction in America’s policies in this region and there are concerns that America is becoming more inward-looking,” he added. “And that raises the question of what Japan should do in these new circumstances.”

Trump has suggested that instead of the US stationing troops in Japan and South Korea, both Tokyo and Seoul should take more responsibility for their own defence. And that, the president has said, would include the two nations developing their own nuclear arsenals.

The Trump administration is also exerting pressure on both Tokyo and Seoul to cover more of the cost of their defence, with US officials informing Japan that its annual bill will rise from US$2 billion a year to US$8 billion for the 54,000 US troops who are presently in Japan, the majority stationed in Okinawa. Seoul is being asked to pay US$5 billion a year, up from less than US$1 billion in 2018.

There are also concerns that Washington’s withdrawal from the Intermediate-range Nuclear Forces Treaty, which was signed by president Ronald Reagan and Soviet secretary general Mikhail Gorbachev in 1987, may lead to additional pressure on Japan to serve as the base for conventional US missiles aimed at targets in mainland Asia.

Gabe said it would not be necessary for the US to station nuclear weapons on Okinawa as it could launch these weapons using its arsenal of long-range missiles, bombers and submarines.

“And if the US did reintroduce them to Okinawa, then that information would probably be leaked and China would consider it to be an act of aggression and retaliate with a build-up of its own capabilities in the region,” he added.

And while the reversion of Okinawa to Japanese control in 1971 was portrayed at the time as a win-win for both Tokyo and Washington, Gabe believes this claim needs to be re-examined.

“The government and scholars have long said it was a win-win situation, but if we look closer, I would say that Japan emerged with less and the US got more,” he said. “They got to keep their nuclear weapons here, and that was a burden on the people of Okinawa.”

The population may not have been aware of the presence of nuclear weapons in the prefecture, but the existence of numerous bases in Okinawa would have made it a prime target in the event of a major conflict in northeast Asia, while residents of Japan’s most southerly prefecture have long complained about the large US military presence and the problems it brings, which range from criminal incidents involving US personnel, to accidents, pollution and noise associated with the bases.