The Paris-based National Council of Resistance of Iran (NCRI) said its sources in the country had confirmed the existence of the military site, codenamed "012", but the group said it could not be certain of what was happening inside the highly secure area.
The NCRI has revealed important aspects of Iran's nuclear programme in the past, including the existence of the Natanz facility in 2002, but experts have met many of its other claims with scepticism.
He said the newly uncovered site was located at the Haft-e Tir military compound, about 10 kilometres (six miles) from the central city of Mobarakeh in Isfahan province.
The site was located inside a 600-metre (650-yard) tunnel, contained four galleries and was heavily guarded, he said.
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Work on the project began in 2005, construction of the tunnels was completed in 2009 and work on facilities at the site "has been nearly completed," he said.
He said the site was being operated by a secret nuclear weaponisation agency known as SPND and run by senior Iranian scientist Mohsen Fakhrizadeh, who it claimed was in charge of the regime's alleged atomic weapons programme.
"Given that this site was built and is supervised by the SPND... There is certainty of the fact this site is linked to the military aspect" of the nuclear programme, Abrishamchi said.
The NCRI could not, however, confirm the purpose of the site.
He said the information had been passed on to French authorities and the Vienna-based International Atomic Energy Agency "in the last few days".
"The clerical regime is in the process of constructing and completing a series of secret sites.... Site '012' is one of them," he said.