That is the question I had, but the following two excerpts suggested that the agreements had become "inoperative" or "obsolete":

It was only in 1991 when the George H. W. Bush administration decided to withdraw all theater and tactical nuclear weapons from the field and from ships that events overtook the transit arrangements.

The Nuclear Vault: Nuclear Noh Drama - Tokyo, Washington and the Case of the Missing Nuclear Agreements

In 1991 former President George H.W. Bush ordered the removal of tactical nuclear weapons from U.S. naval ships (not counting ballistic missile submarines, which do not call on Japanese ports), and from South Korea.

RealClearWorld - Tokyo's Long-Held Secrets Coming Out

Tokyo continued to deny the agreements, even after they became officially inoperative in 1991 as a result of George H. W. Bush's decision to withdraw tactical and theatre nuclear weapons from the field.

Japan 'lied' on secret US nuclear deal | The Australian

The panel's findings prompted Foreign Minister Katsuya Okada to say that he could not rule out the possibility that U.S. ships carrying nuclear weapons made port calls in Japan or transited through Japanese territorial waters.

But the panel said that because of U.S. President George H.W. Bush's 1991 announcement that the U.S. would withdraw tactical nuclear weapons from its naval ships, the port call and transit issue no longer troubles Japan-U.S. ties. The U.S. also maintains a "neither confirm nor deny" policy with regard to the deployment of nuclear weapons.

Secret agreements to get along | The Japan Times Online

In 1991, then US president George Bush announced that US vessels would no longer carry tactical atomic arms, rendering any pact with Japan allowing US nuclear-armed ships to visit obsolete.

Japan-US secret nuclear deal discovered: reports | Nuclear Weapons News at DefenseTalk

Though successive LDP governments, which had ruled for over half a century, had full knowledge of the secret pact at least up to 1989, it was kept under wraps all these years. It was only in June 2009 when former Vice Minister of Foreign Affairs Ryohei Murata revealed that "each foreign minister was briefed (on the secret agreement) in writing by the vice minister." The documents made public by the panel of experts of the MOFA on 9 March 2010 confirmed that senior MOFA officials briefed successive administrations at least up to the Cabinet of former Prime Minister Kaifu Toshiki in 1989. The panels revealed that the briefing document was created on 27 January 1968 by then Foreign Ministry American Bureau chief Togo Fumihiko and contained a detailed account of the American interpretation of the secret agreement.

The briefing document is significant because successive prime ministers and foreign ministers had noted in the margins the date and time they received the document with the word "read" or "verbally briefed". The last entry is dated 24 August 1989 by then Vice Foreign Minister Kuriyama Takakazu, who noted that Kaifu and foreign minister Nakayama Taro were briefed. No further notings had been made since 1993 when a non-LDP government assumed power for a short period of nine months.

One argument is that the gap between 1989 till the present was probably because the Cold War ended in 1991 and the common "enemy" - the USSR - no more existed and President George H.W. Bush may have halted deployment of nuclear weapons on US vessels in 1991.

Testing Times for the Japan-US Alliance: "Secret Pact" Revealed | Institute for Defence Studies and Analyses

And yet, in an editorial last December, the 朝日新聞 Asahi Shinbun asked precisely the same question that I had:

... it is more important for Tokyo to confer with Washington and come up with a unified stand on whether the 1969 pact is still legally binding today.

There is a big difference between today and 40 years ago in the security environment and the nuclear weapons operating strategy. In practical terms, there is a bare possibility of the United States requesting Japan to allow the re-entry of nuclear weapons today.

Still, it would be wrong to leave unattended the conflict between the secret deal and the three non-nuclear principles. Failure to face this problem could shake the public's faith in the Japan-U.S. alliance.

Especially now that Hatoyama's waffling on the Futenma issue is straining Japan-U.S. ties, the government must act wisely.

asahi.com（朝日新聞社）：EDITORIAL: Secret nuclear accord | The Asahi Shimbun, Dec. 23 (IHT/Asahi: December 24,2009

Masanobu Inoue of the Japan Association of Lawyers Against Nuclear Arms (and thus someone clearly not unprejudiced on the issue) argues that the agreements are in fact still in effect:

As is widely known, under the George H. W. Bush (Bush 41) administration in 1991, the US removed all strategic nuclear weapons deployed abroad, and cancelled the nuclear mission of the Marines, naval aircraft, and warships. Does that mean the secret agreements on nuclear arms introduction are already something of the past? That is in fact being discussed in Japan, but the agreements are still very much alive. Even now the US maintains the nuclear missions of some Air Force units and some nuclear-powered submarines, and submarines so tasked visit Japanese ports. In a contingency, it is certain that nuclear weapons would be deployed to these submarines and Air Force units, and that nuclear weapons would be brought into Japan. The US still upholds its NCND ["neither confirm nor deny"] policy.

That the Japanese government knows best that nuclear weapons could be brought into Japan is proved by the following fact. On April 1, 2009 the Congressional Commission on U.S. Strategic Posture (chaired by former Secretary of Defense William J. Perry) submitted a report. It is believed that his report will heavily influence the review of the US nuclear posture being conducted by the Obama administration. In preparing its report, the commission conferred closely with the governments of allies and friendly nations. At the end of the report is a list of the people from each government with whom the commission conferred, and the names of four diplomatic officials at the Japanese Embassy in the US are given first as Japanese government officials. After Japan come other countries including Denmark, Turkey, Germany, France, and Israel. The officials at the Japanese Embassy in the US submitted a three-page memorandum stating the Japanese government's position, apparently telling the commission that Japan opposes the decommissioning of the nuclear cruise missiles deployed on a nuclear-powered submarine scheduled for decommissioning in 2013, and making these requests: low-yield earth penetrating nuclear weapons enhance the reliability of the nuclear umbrella; Japan wants prior consultation on the decommissioning of submarine-launched nuclear Tomahawk missiles; and Japan wants details on nuclear forces and tactical nuclear plans. This shows that not only does the Japanese government consent to bringing nuclear weapons into Japan under the secret agreements, but also desires it, the reason being that it maintains the effectiveness of the nuclear deterrence policy, which is the centerpiece of Japan's security policy.

The reality is that the secret agreements on introducing nuclear weapons even now continue to limit Japan's sovereignty. As having territorial waters of 12 nautical miles was already taken for granted internationally during negotiations for the United Nations Convention on the Law of the Sea (UNCLOS), in 1977 the Japanese government enacted the Territorial Waters Act and set Japan's territorial waters to 12 nautical miles. At the same time it set territorial waters to three nautical miles in the straits of Soya (La P?rouse), Tsugaru, and Tsushima. Even though both sides of these straits are Japanese territory, the territorial water limits were set at three nautical miles, which made parts of the straits into international waters, and is highly unusual from an international point of view. Why was this done?

Before these lines were drawn, the US was concerned that if the 12 nautical miles from shore were another country's territory under UNCLOS, it would limit the free movement of nuclear submarines and impose a serious impediment on the performance of plans for nuclear war in accordance with the Single Integrated Operational Plan (SIOP). This was because although submarines have the right of innocent passage in other countries' territorial waters, they must do so by surfacing and hoisting their national flags, which would make it impossible for nuclear submarines to carry out their tactical nuclear missions. The US lobbied the Japanese government intensively. To Japan's government there was also the concern that if strategic and attack nuclear submarines were to pass through these straits while surfaced, it would create a serious political problem because the submarines would be seen as openly bringing nuclear weapons into Japan. Hence the choice made by the Japanese government, which was bound by the secret agreements on introducing nuclear weapons, was to give those straits exceptional treatment. Even now, the waters in these straits beyond three nautical miles from shore are international.

Japan's government changed and is now administered by the Democratic Party of Japan (DPJ). Foreign Minister Katsuya Okada sent a letter to US Secretary of State Hillary Clinton and stated that Japan does not oppose the decommissioning of nuclear-armed Tomahawk cruise missiles. On March 9 the DPJ administration released the results of its investigation of the secret agreements. Foreign Minister Okada then expressed the view that the secret agreements are an issue of the past because, owing to the 1991 Bush initiative, it is no longer possible to conceive of a situation in which nuclear weapons are brought into Japan. Prime Minister Yukio Hatoyama stated that the three non-nuclear principles would continue to be observed. However, it is quite possible that nuclear weapons would be introduced in the event of armed conflict in the Japan region. As the introduction of nuclear weapons is still possible, if the government's stance is to observe the three non-nuclear principles, the government must properly provide for consistency with US policy for introducing nuclear weapons in a contingency. The DPJ claims that the secret agreements are a problem of the past, and that the introduction of nuclear weapons from now on is impossible, thereby doing nothing about the contradiction between US nuclear policy and the three non-nuclear principles. This DPJ posture could create the departure point for a new secret pact.

Japan's future security policy is being called squarely into question.

On the Secret Nuclear Agreements | Japan Association of Lawyers Against Nuclear Arms - 2010 May 14

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