The issue reached Greece's parliament last week after Frangiscos Ragoussis, a criminal lawyer, said seven Pakistani immigrants were abducted from their homes in central Athens, blindfolded and taken to a secret location in late July.
There, Ragoussis said, they were questioned for their alleged involvement in or links to the bombings, in which 56 people died.
He claimed that at least another 21 Pakistanis from other parts of Greece, in the eastern city of Ioannina and Oinofyta, near Athens, received similar treatment.
Ragoussis said that police and other government officials buried the file when the allegations first surfaced in summer.
"New evidence should come forward in the next few days which will prove that my clients were abducted and tortured and why for months there was no progress with the investigation," Ragoussis said.
"The government was very quick to accuse these men of being liars – even before the investigation was completed."
The allegations automatically triggered a preliminary investigation by prosecutors in Athens and answers from the justice minister.
Dimitris Papangelopoulos, the prosecutor responsible for overseeing an inquiry into the allegations, said his office had the "guts" to get to the bottom of the claims.
Speaking after meeting, Dimitris Linos, the Supreme Court prosecutor, said that if police officers had acted improperly they would be prosecuted.
Giorgos Voulgarakis, the public order minister, denied the allegations which he said lacked any credible basis and that such an operation involving foreign intelligence officials had not taken place on Greek soil.
"We have denied these accusations since they first surfaced in August"
public order minister
"We have denied these accusations since they first surfaced in August," he said.
Voulgarakis said the Pakistani ambassador to Athens had informed him that there were no such complaints from any of the 35,000 Pakistanis living in Greece.
A source at the Public Order Ministry, who asked not to be named, said: "A covert operation of this type did not happen and at no time did British authorities request the help of Greek security services to investigate Greek or foreign individuals suspected of being involved in the London bombings."
The Public Order Ministry said it had not received any official complaint about the alleged incident until last week.
Pakistani formal complaint
However, Javed Aslam, the president of the Pakistani Community in Athens, said he filed a formal complaint with the authorities on 29 July on behalf of the seven immigrants. He said the English-speaking interrogators' main questions concerned telephone calls to England.
"They threatened the men not to say anything once they were released or else their families would be targeted," he said. "We will not stop until we find justice."
Lawyers for migrants and refugees in Greece said this was not the first time many of the 130,000 Muslims living in Greece have been subjected to this sort of treatment by Greek and foreign security officials.
Alexander Giotopoulos, the head
of November 17
In the run-up to the 2004 Olympics in Athens, Amnesty International expressed concerns about reports that refugees, migrants and asylum-seekers were being rounded up and detained during the biggest security operation in the history of the Games.
Hundreds of makeshift mosques scattered around the capital were subjected to surveillance and police mounted mass document checks and inspections.
Vassilis Papdopoulos, a lawyer representing refugees, said: "We have a serious problem if the government is tolerating this to happen on its own soil."
Alekos Alavanos, the president of Greece's opposition Synasprosmos party, said Greece used security for the 2004 Olympics as a pretext systematically to break international treaties on the rights of refugees.
He said: "We saw that during the crackdown on members of terrorist group November 17 and during the Olympics in Athens, British Intelligence officials were actively involved with the security of this country.
"Taking this into consideration, it is unbelievable that the Public Order Ministry is now saying that what happened to these Pakistani men is a fantasy."
The British embassy in Athens has rejected the allegations that it led a covert operation of this type. The embassy said it would not enter into media speculation about the alleged operations of the UK's security and intelligence services, and described the case as far-fetched.
British-Greek co-operation on security issues goes back several years.
Scotland Yard worked with its Greek counterparts to track down members of Greek terrorist group, November 17, which is blamed for 23 killings and dozens of bombings, after Brigadier Stephen Saunders, a British military attaché, was killed in June 2000.
Fifteen members of the group were tried and given multiple life sentences. The men are appealing against their sentences.