General David Petraeus, the head of US Central Command, today confirmed a US intelligence assessment which said the freed British hostage Peter Moore was "certainly" held in Iran for at least some of his 31 months in captivity.

As Moore arrived back in Britain at RAF Brize Norton this evening, Petraeus told a press conference in Baghdad: "I am on the record as having said that our intelligence assessment is that he certainly spent part of the time, at the very least, in Iran."

The statement puts US intelligence at odds with the British Foreign Office, which today continued to insist there was no evidence that Moore had been held in Iran.

The Foreign Office referred to a report in Wednesday's Guardian – which said the Quds unit of Iran's Revolutionary Guard had played a key role in the abduction of Moore, an IT consultant, and his four guards – as "speculation".

The four guards were killed by their captors. Three of the bodies have been returned and the remains of the fourth victim, Alan McMenemy, are expected to be returned soon.

Although Petraeus, who commands the US military effort in Iraq and Afghanistan, confirmed Moore had been taken to Iran, he was quoted by Reuters as saying: "It is difficult to say what role the Revolutionary Guards, and in particular the Quds force element, played in that."

Moore's release came on the same day as the transfer of Qais al-Khazali, the head of an Iranian-backed Shia group which claimed responsibility for the kidnapping, from US to Iraqi custody.

Petraeus said the transfer had been carried out according to an agreement with the Iraqi government which said the US had to release its detainees or hand them over to Iraq by the end of last year.

However, a representative of Asaib Ahl al-Haq, al-Khazali's group, and an Iraqi member of the negotiating team that helped secure Moore's release, told the Associated Press Moore had not been released until the group received confirmation that its leader had been transferred.

In a statement issued by the Foreign Office this evening, Moore's step-parents Fran and Pauline Sweeney said: "We are thrilled to have Peter back safely. We have a lot of catching up to do and would like to have time with Peter on our own. We would now ask the media to give us space and privacy."

A Foreign Office spokesman said: "Peter was met by Foreign Office staff and will be reunited with his family later. Peter and his family have asked for privacy at this time."