Israel’s nuclear program began in 1959. In 1958, Israel secretly initiated work at what was to become the Dimona nuclear research site. In 1961, the CIA estimated that Israel could produce nuclear weapons within the decade.

The discovery presented a difficult challenge for US policymakers. The Kennedy and Johnson administrations fashioned a complex scheme of annual visits to Dimona to ensure that Israel would not develop nuclear weapons. But the Israelis were adept at concealing their activities. By late 1966, Israel had reached the nuclear threshold, although it decided not to conduct an atomic test.

By the time Prime Minister Levi Eshkol visited President Lyndon Johnson in January 1968, the official State Department view was that despite Israel’s growing nuclear weapons potential, it had “not embarked on a program to produce a nuclear weapon.” That assessment, however, eroded in the months ahead. By the fall, Assistant Defense Secretary Paul Warnke concluded that Israel had already acquired the bomb when Israeli Ambassador Yitzhak Rabin explained to him how he interpreted Israel’s pledge not to be the first country to introduce nuclear weapons into the region. According to Rabin, for nuclear weapons to be introduced, they needed to be tested and publicly declared. Implicitly, then, Israel could possess the bomb without “introducing” it.

The question of what to do about the Israeli bomb would fall to Nixon. Though Nixon and his national security adviser, Henry Kissinger may have been inclined to accommodate Israel’s nuclear ambitions, they would have to manage senior State Department and Pentagon officials whose perspectives differed. Documents prepared between February and April 1969 reveal a great sense of urgency and alarm among senior officials about Israel’s nuclear progress.

As Defense Secretary Melvin Laird wrote in March 1969, these “developments were not in the United States’ interests and should, if at all possible, be stopped.” Above all, the Nixon administration was concerned that Israel would publicly display its nuclear capabilities.

Apparently prompted by those high-level concerns, Kissinger issued NSSM (National Security Study Memorandum) 40 — titled Israeli Nuclear Weapons Program — on April 11, 1969. In it he asked the national security bureaucracy for a review of policy options toward Israel’s nuclear program. In the weeks that followed, the issue was taken up by a senior review group (SRG), chaired by Kissinger, that included CIA Director Richard Helms, Undersecretary of State Elliot Richardson, Deputy Defense Secretary David Packard and Joint Chiefs Chairman Earle Wheeler.

The one available report of an SRG meeting on NSSM 40 suggests that the bureaucracy was interested in pressuring Israel to halt its nuclear program. When Richardson and Packard summoned Rabin on July 29 to discuss the nuclear issue, Richardson posed three issues for Rabin to respond to: The status of Israel’s NPT deliberations; assurances that “non-introduction” meant “non-possession” of nuclear weapons; and assurances that Israel would not produce or deploy the Jericho ballistic missile. Rabin, however, was unresponsive except to say that the NPT was still “under study.”

Nixon and Israeli Prime Minister Golda Meir would have to address the nuclear issue when they met in late September 1969. Perhaps the most fateful event of this tale was Nixon’s one-on-one meeting with Meir in the Oval Office on Sept. 26, 1969.

In later years, Meir never discussed the substance of her private conversation with Nixon, saying only, “I could not quote him then, and I will not quote him now.” Yet, according to declassified Israeli documents, since the early 1960s, Meir had been convinced that “Israel should tell the United States the truth (about the nuclear issue) and explain why.”

Even without the record of this meeting, informed speculation is possible. It is likely that Nixon started with a plea for openness. Meir, in turn, probably acknowledged — tacitly or explicitly — that Israel had reached a weapons capability, but probably pledged extreme caution. (Years later, Nixon told CNN’s Larry King that he knew for certain that Israel had the bomb, but he wouldn’t reveal his source.) Meir may have assured Nixon that Israel thought of nuclear weapons as a last-resort option, a way to provide her nation with a psychological sense of existential deterrence.

Subsequent memorandums from Kissinger to Nixon provide a limited sense of what the national security adviser understood happened at the meeting. Kissinger noted that the president had emphasized to Meir that “our primary concern was that the Israeli (government) make no visible introduction of nuclear weapons or undertake a nuclear test program.” Thus, Israel would be committed to conducting its nuclear affairs cautiously and secretly; their status would remain uncertain and unannounced.

On Feb. 23, 1970, Rabin told Kissinger privately that he wanted the president to know that, in light of the Meir-Nixon conversation, “Israel has no intention to sign the NPT.”

Kissinger informed Nixon that he told Rabin that he would notify the president. And with that, the decade-long US effort to curb Israel’s nuclear program ended.

That enterprise was replaced by understandings negotiated at the highest level, between the respective heads of state, that have governed Israel’s nuclear conduct ever since.

That so little is known today about the tale of NSSM 40 is not surprising. Yet, even as Nixon and Kissinger enabled Israel to flout the NPT, NSSM 40 allowed them to create a defensible record. As was his typical modus operandi, Kissinger used NSSM 40 to maintain control over key officials who wanted to take action on the problem.

Politically, the Nixon-Meir agreement allowed both leaders to continue with their old public policies without being forced to openly acknowledge the new reality. As long as Israel kept the bomb invisible — no test, declaration or any other act displaying nuclear capability — the United States could live with it.

Over time, the tentative Nixon-Meir understanding became the foundation for a remarkable US-Israeli deal, accompanied by a tacit but strict code of behavior to which both nations closely adhered. Even during its darkest hours in the 1973 Yom Kippur War, Israel was cautious not to make any public display of its nuclear capability.

Yet set against contemporary values of transparency and accountability, the Nixon-Meir deal of 1969 now stands as a striking and burdensome anomaly. Israel’s nuclear posture is inconsistent with the tenets of a modern liberal democracy. The deal is also burdensome for the United States, provoking claims about double standards in US nuclear nonproliferation policy.

— Avner Cohen is a senior research fellow at the Center for International and Security Studies at the University of Maryland; William Burr is a senior analyst at the National Security Archive at George Washington University.