It is unclear how Mr. Amiri’s information fed into the 2007 intelligence estimate. That document contended that Iran halted its design work on a nuclear weapon in 2003. A new national intelligence estimate, which has been repeatedly delayed this year, is likely to back away from some of the conclusions in the earlier document. For example, American intelligence officials now believe the design work on a weapon was resumed and continues to this day, though likely at a slower pace than earlier in the decade.

Mr. Amiri, a specialist in measuring radioactive materials, is not believed to have been central to any of Iran’s efforts at weapons design. But he worked at the Malek Ashtar University, which some American officials think is used as an academic cover for the organization responsible for designing weapons and warheads that could fit atop an Iranian missile. Those operations are run by Mohsen Fakhrizadeh, an Iranian academic with long and close ties to the Islamic Revolutionary Guards Corps. Mr. Fakhrizadeh, United States officials maintain, is now effectively the head of the university, and in an effort to evade international inspectors has reorganized the structure of the Iranian program.

The National Council of Resistance of Iran, an opposition group based in France, in 2004 disclosed the existence of what it called a secret administrative headquarters for the military aspects of the Iranian program. The group made public more information in 2008, saying the site was in a suburb of Tehran adjacent to the university, giving it academic cover, and was called Mojdeh, after an adjacent street.

Mohammad Mohaddessin, head of the group’s foreign affairs committee, said the school “does not operate like a university.” Instead, he said, it is “a center for research and development of weapons” and works in cooperation with the Mojdeh site.

The American officials said that at some point while working as a secret informant, Mr. Amiri visited Saudi Arabia, and the C.I.A. arranged to spirit him out of that country and eventually to the United States, where he settled in Arizona. It is unclear whether Mr. Amiri tried to bring his wife and child with him.

Administration officials conceded that Mr. Amiri’s decision to come out of hiding and return to Iran was both a large embarrassment and a possible disincentive to future defections.

But the incident is also an embarrassment for Iran. Analysts said that even if he is publicly greeted as a hero, Mr. Amiri will probably be viewed with suspicion by the Iranian government.