The dissident group said the Tehran-based Organisation of Defensive Innovation and Research (SPND) was "the nerve center of the militarisation of the Iranian nuclear program," which has been responsible for "the design and manufacture of the atomic bomb."
"The transfer of the SPND was completed in July," said the Paris-based National Council of Resistance of Iran (NCRI), which has made significant revelations about Iran's nuclear programme in the past.
"Managers and key services were relocated to secret locations, while some administrative officials were left in place to deceive IAEA inspectors," said dissident leader Afchine Alavi.
The SPND was targeted in August by a new round of US sanctions against companies and individuals seen as providing support to illicit Iranian nuclear activities.
The brains behind the SPND, Mohsen Fakhrizadeh, sought for years by the International Atomic Energy Agency (IAEA), is being "hidden by the regime", the NCRI said in a report.
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"This game of hide-and-seek with the IAEA proves that the regime has no intention of abandoning the military aspect of its programme and that it does not want to be transparent."
Negotiations between Iran and world powers over its controversial nuclear programme are due to resume next week in Vienna.
Iran and the P5+1 group of nations (China, the United States, France, Britain, Russia and Germany) have set a November 24 deadline to strike a deal guaranteeing that Tehran's nuclear programme is used for exclusively peaceful means.
But talks have stalled over the issue of Iran's future capacity for uranium enrichment and the timetable for lifting international sanctions against Tehran.
The IAEA regularly inspects Iran's nuclear facilities, but it also suspects that Tehran's programme had "possible military dimensions" before 2003 and possibly since.
Iran insists its nuclear programme is entirely peaceful.