VIENNA — Iran was actively designing a nuclear weapon until 2009, more recently than the United States and other Western intelligence agencies have publicly acknowledged, according to a final report by the United Nations nuclear inspection agency.
The report, based on partial answers Iran provided after reaching its nuclear accord with the West in July, concluded that Tehran conducted “computer modeling of a nuclear explosive device” before 2004. It then resumed the efforts during President Bush’s second term and continued them into President Obama’s first year in office.
But while the International Atomic Energy Agency detailed a long list of experiments Iran had conducted that were “relevant to a nuclear explosive device,” it found no evidence that the effort succeeded in developing a complete blueprint for a bomb.
In part, that may have been because Iran refused to answer several essential questions, and appeared to have destroyed potential evidence in others.
The report, issued here Wednesday evening to the 167 countries that make up the board of the agency, is intended to complete a decade-long attempt to determine what kind of progress Iran made toward the technological art of designing a warhead that could fit atop a nuclear missile.
The completion of the report is one of the steps that Iran had to take — along with dismantling centrifuges and shipping nuclear fuel out of the country — before sanctions will be lifted under the nuclear deal.
Mr. Obama and his secretary of state, John Kerry, concluded this year that it was more important to secure a deal that will, if carried out fully, prevent Iran from gaining the material to build a bomb for at least 15 years than making it admit to past activities. So, the report’s publication allows the deal to go through, no matter how definitive or inconclusive the final result.
But Iran’s refusal to cooperate on central points could set a dangerous precedent as the United Nations agency tries to convince other countries with nuclear technology that they must fully answer queries to determine if they have a secret weapons program.
The agency’s bottom-line assessment was that Iran had made a “coordinated effort” to design and conduct tests on nuclear weapon components before 2003 — echoing a United States national intelligence estimate published in 2007 — and that it had conducted “some activities” thereafter.
“These activities did not advance beyond feasibility and scientific studies” and the acquisition of technical capabilities, the agency concluded. The efforts ended after 2009, or just as Mr. Obama was taking office and accelerating the sanctions and cybersabotage program against Iran’s nuclear facilities that ultimately brought Iranian officials to the negotiating table.
Tehran gave no substantive answers to one quarter of the dozen specific questions or documents it was asked about, leaving open the question of how much progress it had made.
The report, titled “Final Assessment of Past and Present Outstanding Issues Regarding Iran’s Nuclear Program,” will not satisfy either critics of the nuclear deal or those seeking exoneration for Iran. Instead, it draws a picture of a nation that was actively exploring the technologies, testing and components that would be needed to produce a weapon someday. However, it does not come to a conclusion about how successful that effort was.
The agency’s director, Yukiya Amano, said last week that the document would not be “black and white,” and that assessment proved correct.
Nothing in the report suggests that Iran will prevent the I.A.E.A. from monitoring its production of nuclear fuel for the next decade and a half, the crucial element of the July agreement. But Iran’s refusal to answer some of the questions also does not portend well for transparency about its activities.
At Iran’s Parchin complex, where the agency thought there had been nuclear experimental work in 2000, “extensive activities undertaken by Iran” to alter the site “seriously undermined” the agency’s ability to come to conclusions about past activities, the report said.
Diplomats familiar with the compilation of the report said the inspectors met “experts” in Iran, but would not say if they met the leader of the nuclear effort, Mohsen Fakhrizadeh. (Other diplomats said Mr. Fakhrizadeh was definitely not among those the inspectors met.) One diplomat said Iran had said it feared that the scientists could be assassinated if they were identified. The agency said inspectors were able to visit two workshops.
Time and again, the I.A.E.A. seemed close to rejecting Iranian arguments that its experimentation was for civilian purposes. The inspectors found that Iran’s nuclear program was “suitable for the coordination of a range of activities relevant to the development of a nuclear explosive device” and that its experiments had “characteristics relevant to a nuclear explosive device.”
In one or two areas, notably a document provided by Western intelligence agencies indicating that Iran was looking at how to make uranium metal, a step needed for a weapon, it found “no indication of Iran having conducted activities” related to the document.
Recently, as the report’s publication approached, Iran’s position of complete denial that it had sought a bomb seemed to soften. In October, a former Iranian president, Ali Akbar Hashemi Rafsanjani, told journalists in Tehran that the nation had considered making nuclear arms during its war with Iraq in the 1980s but backed away.
“We sought to have that possibility for the day that the enemy might use a nuclear weapon,” he was quoted as saying. “That was the thinking. But it never became real.” He said nothing about what happened up to 2004 or the more sporadic efforts beyond.
The issues the I.A.E.A. addressed in Wednesday’s report date back a decade. Starting around mid-2004, thousands of pages of detailed evidence of Iran’s suspected research on how to design a weapon were collected by intelligence agencies in the United States, Israel and Europe, and eventually turned over to the agency’s inspectors here in Vienna.
Some of the evidence came from a laptop computer smuggled out of Iran by a person American and German officials identified as an Iranian technician, who had access to some of the most sensitive results from two secret Iranian nuclear projects. Both appeared related to different technologies needed to design a nuclear warhead, including the vital process of building a detonation system to fit inside the nose cone of Iran’s Shahab-3 missile, Persian for “shooting star.”
Iran claimed that the documents were fabrications, part of a Western conspiracy to set the groundwork for bombing the country’s nuclear facilities or overthrowing the government. The technician apparently never made it out of the country; he remained in Iran after sending the laptop out with his wife and family.
“We never figured out if he was imprisoned or executed,” a former intelligence officer involved in the operation said in an interview in 2008.
The year before that interview, however, American intelligence experts told the Bush administration about a surprising finding: While Iran once had a full-scale weapons development effort underway, it suspended the project sometime in late 2003, shortly after the American invasion of Iraq.
“Prior to 2003 they had a full-scale Manhattan Project,” said Gary Samore, Mr. Obama’s top nuclear proliferation expert in the first term. After that, he said, the effort was sporadic, even as Iran pressed ahead to build the facilities to produce uranium fuel — the program that was rolled back and frozen by the agreement reached in July.
Even after the 2007 report, though, I.A.E.A. inspectors pressed Iran to address the questions raised in the documents. In 2008, the agency’s chief inspector gathered officials from around the world into a large auditorium here and displayed the evidence to them. This included memos signed by Mr. Fakhrizadeh, the elusive academic who ran the program for the Islamic Revolutionary Guard Corps, and Iranian videos appearing to show how to detonate a weapon in an “air burst,” much as the bomb exploded high over Hiroshima, Japan, in 1945.
In 2011, frustrated that Iran had failed to honor several agreements to answer questions and turn over documents, the atomic agency published a list of a dozen issues — “possible military dimensions,” in bureaucratic jargon — that it had to clear up before it could close Iran’s file.
But as the deal got closer last spring, Mr. Obama and Mr. Kerry had to make a crucial decision: whether it was worth jeopardizing the deal by insisting that Iran must admit to its past activities. From all indications since then, the president seems to have decided that it was more important to get commitments about limiting future activities than to force Iranian officials to admit to a past the country insists never happened.
Mr. Kerry, pressed on the question of Iranian disclosure of past activities by Judy Woodruff on “PBS NewsHour,” said: “They have to do it. It will be done. If there’s going to be a deal, it will be done.” But weeks later, he said United States intelligence agencies already had “perfect knowledge” of Iran’s activities, suggesting that a public confession was not necessary.
The result was a carefully designed diplomatic compromise. Iran had to meet deadlines to turn over documents, but the agreement did not specify how complete the disclosures had to be, whether important scientists had to be interviewed or whether inspectors had to be allowed into the sensitive research sites, including some universities, where the work took place.
Correction: December 2, 2015
An earlier version of this article misspelled the given name of the director of the International Atomic Energy Agency. He is Yukiya Amano, not Yukia.