It issued a warning to media organisations after a leading Athens newspaper identified the British intelligence officer and 15 Greek agents, alleging that they took part in the arrest and abuse of 28 Pakistan-born detainees who were held in connection with the July 7 bombings in London.

The disclosures sparked a row in Athens, with opposition leaders and human rights groups demanding to know why British agents were allowed to operate in Greece.

There are mounting calls for a parliamentary investigation, and George Voulgarakis, the Public Order Minister, faced demands last night to appear before the parliament.

Proto Thema named the British official as the MI6 station chief in Athens. It said that he and a second, unnamed, British agent took part in the interrogation of some suspects, who said that they were hooded and held in secret. One of the migrant workers claims to have had a gun forced into his mouth.

The Foreign and Commonwealth Office last night refused to confirm or deny whether the person named in the Greek press works at the British Embassy in Athens.

British ministers have until now denied that British officials played any part in this counter-terror operation, which allegedly took place days after the July attacks on three Tube trains and a bus in which 52 passengers died. Jack Straw, the Foreign Secretary, told MPs last week that the reports were “complete nonsense”.

Last night Mr Voulgarakis condemned the naming of Greek intelligence officers as “illegal and endangering the safety of our agents in the field”. He said that two of the named agents had been withdrawn from postings in Kosovo. When the allegations emerged a fortnight ago, Mr Voulgarakis also denied that the arrests had taken place.

The migrant workers said that they were questioned by British investigators about mobile telephone calls linked to the four suicide bombers. They said they were also asked about calls made to a suspect in Pakistan whom the British officials apparently wanted to question about the London attacks.

If the Greek Government bows to demands for an investigation, British ministers may have to defend the behaviour of MI6 agents abroad.

Makis Triantafyllopoulos, publisher of Proto Thema, said last night: “The Greek and British governments have been lying from the start.”

Some of the detainees have now given evidence to a magistrate about their treatment. One, Muhammad Munir, claims he was held incommunicado for six days and “hit very hard on the head”. He and others said that they were sure the figures questioning them were British, yet all of them spoke fluent Greek. They described “a black British case officer” as taking part in their interrogation.

Most of the 28 men are too frightened to complain about their treatment, saying that they were threatened by the British officers that their families in Pakistan and Britain would suffer if they spoke about the interrogation.

Those who have been persuaded by Pakistani community leaders to give evidence claim they were seized at the homes at night, hooded and driven to secret locations. Some are alleged to have been held at EYP, the headquarters of Greek intelligence.

Gul Nawaz, who has lived in Athens for three years, said in his deposition: “Twice a policeman hit me while I was on the floor. I asked him for some water and he punched me in the face. They took my mobile phone. They wanted to know about my friends in London and relatives and phone calls.”

He was asked if he had any links to al-Qaeda. “I said I didn’t know. I said I’m just a Muslim and I work to send money to my wife and three children in Pakistan. I never called anybody in London.”

The Greek newspaper claims that Costas Karamanlis, the Prime Minister, sanctioned the British-led operation. It names two officials working in his office as taking part in negotiations over this incident. Anastasis Papaligouras, the Greek Justice Minister, has ordered an investigation into the affair.

• The US Embassy in London has clarified remarks by Robert Tuttle, the Ambassador, after he told the Radio 4 Today programme that there was no evidence that terrorist suspects were taken to Syria under the process of “special rendition”. The embassy acknowledged that there had been reports of a rendition to Syria, but refused to comment further.

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