Iran's supreme leader, Ayatollah Ali Khamenei, was directly involved in the disappearance of the two main leaders of the Green movement, an opposition website has claimed.

Mehdi Karroubi and Mir Hossein Mousavi have not been seen in public since being put under house arrest following renewed street protests in mid-February when thousands of Iranians, inspired by the uprisings in the Arab region, took to the streets in defiance of warnings from the regime. They are believed to have been arrested on 26 February.

Karroubi's official website, Sahamnews.net, said Khamenei had ordered what it described as "the abduction of Karroubi and his wife, Fatemeh".

The site said Khamenei's administrative adviser, Vahid Haghanian, commanded the security forces which raided Karroubi's house in north Tehran and confiscated his belongings.

"On the night of the kidnapping, Vahid, a top official in the supreme leader's office, was present in Mr Karroubi's house and he personally commanded the whole operation of evicting Mr Karroubi and his wife from their own house and taking them to an unknown location," the website said.

"We believe that the supreme leader himself is responsible for this kidnapping and Vahid was appointed by him to carry out the operation."

The website said Haghanian advises the supreme leader on internal affairs.

Since the disappearances, Iranian officials have given vague and often contradictory statements about Karroubi, Mousavi and their wives.

A spokesman for Iran's judiciary, Gholam-Hossein Ejei, confirmed initially that restrictions had been imposed on opposition leaders but later denied they had been arrested. "Reports ... about the transfer of Karroubi and Mousavi to a prison are not correct and are rejected," he said on Tuesday last week. Tehran prosecutor Abbas Jafari Dolatabadi said talk of imprisonment was a "sheer lie" and added: "Mr Mousavi and Karroubi, along with their wives, are in their homes."

Meanwhile, Mousavi's daughters wrote on opposition website Kaleme.org that they cannot visit their parents. "We read the news that our parents are not under house arrest and they are not prisoners ... which meant that we, their children, can see them ... But this was not the case. We went to our parents' home, and from the iron gate installed at the entrance of the alley to their home we were stopped by the security, who said that 'you can't go, the news [that you can visit] is wrong'."

Karroubi's sons told Sahamnews.net that they have repeatedly visited Karroubi's house but no one was there. They also said that neighbours claim they have witnessed Karroubi and his wife being taken out of their house.

Ardeshir Amir-Arjomand, a spokesman for Mousavi, told the Guardian: "Their situation is worse than a prisoner because when someone is jailed, at least you know who has jailed him or where he has been taken to. But in the case of Karroubi and Mousavi, no one takes responsibility or even admits they have been arrested."

Rumours were rife in recent weeks that the two had been taken to Heshmatieh prison in east Tehran.