An Iranian nuclear scientist who claimed to have been abducted by the CIA and who returned to a hero's welcome in Tehran in July has been imprisoned and tortured on suspicion of giving away state secrets, according to an opposition website.

Iranbriefing.net – run by a US-based group that normally reports on political prisoners and the activities of Iran's revolutionary guard – said the scientist, Shahram Amiri, had been interrogated intensively for three months in Tehran before spending two months in solitary confinement, where his treatment left him hospitalised for a week.

The Tehran authorities would not confirm or deny the account. Asked to comment, a spokesman for Iran's judiciary said: "I haven't heard anything about this [his arrest] and I don't have any information regarding this matter."

Amiri has not been seen in public in the six months since his much-publicised homecoming from America, where he claimed to have been held against his will. State media portrayed him at the time as a daring patriot who had escaped from his alleged CIA captors with critical information about US covert operations against Iran.

US officials, surprised by Amiri's unexpected return to Iran, insisted he had gone to the US willingly. However, there was concern in US intelligence circles that his original "defection" in Saudi Arabia in 2009 could have been a trap to embarrass the CIA and trick its officials into revealing how much the US knows about the Iranian nuclear programme.

The evidence is contradictory. During his time in the US, Amiri appeared to have made three videos – one saying he had decided to continue his studies in the US, another saying he was being held captive and a third claiming to be on the run from the CIA. He then presented himself to the Iranian interest section at the Pakistani embassy in Washington, asking to go home.

Independent but unverified reports from inside Iran said Amiri's family had been stripped of their passports and placed under close scrutiny after the scientist went missing on his pilgrimage to Mecca.

Western observers said his disappearance from public view since last summer strengthened their view that he had been forced to return by threats to his relatives. It is not yet clear whether a planned Iranian television drama based on the official version of his story will be aired as scheduled this year.

Amid the conflicting reports, it is clear that the struggle over Amiri is just one more battle in an increasingly ferocious secret war over Iran's nuclear programme that has seen two other Iranian scientists assassinated and a third injured in bomb attacks last year.

Iran has blamed western and Israeli intelligence for the attacks, and for a computer worm, known as Stuxnet, that caused centrifuges to malfunction at its uranium enrichment plant in Natanz.

Tehran also claimed last week that General Ali Reza Asgari, a former revolutionary guard commander and deputy defence minister who disappeared in Istanbul just over four years ago, was being held in an Israeli prison. Mohammad Raouf Sheybani, a deputy foreign minister, called for an international inquiry into Asgari's fate.

Covert operations against Iran's nuclear programme appear to have had some success in slowing it down. The main enrichment plant in Natanz stopped processing uranium altogether for a few days in November. But diplomatic efforts to persuade Tehran to suspend its programme in return for foreign technical and financial assistance have so far failed.

Talks in December between Iran and six major powers in Geneva led only to an agreement to meet again, in Turkey later this month. Tehran has invited selected foreign diplomats to tour some of its nuclear facilities ahead of the meeting. But the US, which is not invited, has dismissed the invitation as a propaganda ploy.