Greek public order minister George Voulgarakis has told MPs there is no truth in claims by 28 Pakistanis that they were kidnapped for interrogation.
The Pakistanis say they were held after the 7 July London bombings
Mr Voulgarakis said the government had no need to resort to what he called James Bond-style methods.
The Pakistanis say they were detained in Greece after the London bombings of 7 July, held for several days without access to a lawyer and mistreated.
The UK government has denied reports that a British MI6 agent was involved.
Mr Voulgarakis also accused newspapers which had published the names of Greek intelligence agents of putting them and their families in danger.
The Greek weekly paper Proto Thema earlier published what it said was the name of a British spy chief and 15 Greek agents involved in the abduction and abuse of the migrants.
The UK government has forbidden the British media from naming the man.
Mr Voulgarakis said the Greek security services had checked more than 5,000 foreigners after the British government asked all European Union countries to assist with the investigation into the London suicide bombers who killed 52 people in July 2005.
But he insisted that "secret agreements and protocols did not exist". "Everything was done legally," he said.
A Greek security task force had "found nothing worrying" in phone records examined during the anti-terror investigation, Mr Voulgarakis said.
The BBC's Malcolm Brabant in Athens says Greek opposition politicians remain deeply dissatisfied with the response of the UK and Greek governments to the allegations.
Mr Voulgarakis' deputy, Christos Markoyiannakis, resigned on Tuesday after publicly criticising a senior judge investigating the case.
The Pakistanis said they had hoods placed over their heads and that they were held for up to seven days without access to a lawyer. Some of them also claim that they were beaten.