The political storm over allegations of MI5 complicity in torture escalated tonight after Alan Johnson, the home secretary, accused the media of publishing "groundless accusations" and commentators of spreading "ludicrous lies" about the Security Service.

As defence lawyers prepared to challenge the government's success in suppressing severe criticism of MI5 officers made by one of Britain's most senior judges, the Liberal Democrat leader, Nick Clegg, pointed the finger at the "very top of government" saying senior ministers had probably known about claims of Britain's involvement in torture but failed to take action to stop it.

The home secretary's intervention came as Kim Howells, the chairman of the parliamentary Intelligence and Security Committee (ISC), came out in support of Jonathan Evans, the director general of MI5, dismissing any suggestion that he had been misled by the Security Service. He said he had seen no evidence that MI5 had colluded in torture.

That is at the centre of this week's appeal court ruling, which disclosed CIA-based intelligence showing that MI5 knew that British resident Binyam Mohamed had been subjected to treatment "at the very least cruel, inhuman, and degrading".

The appeal court, presided over by the Lord Chief Justice Lord Judge, also referred to a recent US court case where the judge vindicated Mohamed's claims that "UK authorities" had been "involved in and facilitated the ill-treatment and torture" to which he was subjected while under the control of the US.

But it was a passage written into the draft judgment by Lord Neuberger, the Master of the Rolls, referring to MI5 officers having "deliberately misled" parliament and sharing a "culture of suppression" which prompted Jonathan Sumption QC to demand its removal. The phrases are contained in Sumption's letter which has been released.

Evans contested the allegations in an article in today's Daily Telegraph. But in a carefully-worded passage wrote: "We did not practise mistreatment or torture and do not do so now, nor do we collude in torture or encourage others to torture on our behalf." Johnson repeated these words in a BBC interview, adding: "People can make their arguments and their assertions, but that shouldn't be taken by some commentators in the media as true simply because someone has said it's true."

The home secretary accused the former Tory shadow home secretary David Davis of spreading a "gross and offensive misrepresentation of the truth" and called on his party's leadership to distance itself from the remarks.

In a BBC interview on Thursday, Davis said there were 15 other cases which suggested a culture of collusion or complicity in torture by MI5 and MI6. He said the alleged mistreatment of Binyam Mohamed – who says his genitals were repeatedly cut, and he was hung by his wrists and beaten until he was sick – "seems like something the Gestapo got up to".

Clegg demanded to know if ministers were told the US had changed its rules on torture after the 9/11 attacks. Either the government knew, or the Security Service was engaged in a cover-up, he claimed. He said: "We must know who in Britain knew the US had changed the rules on torture, when they knew and what action they took. We can only conclude that the Security Services either kept the information to themselves, or they informed ministers who failed to act immediately. "Both of these would suggest at best a cover-up and at worst collusion in torture. Knowledge of Britain's potential complicity in torture looks likely to have gone to the very top of government," he said.

Responding to court evidence that MI5 had withheld documents from the ISC, Howells said Evans had contacted him on Thursday to assure him that MI5 had not withheld from the committee documents relating to Mohamed's treatment by the US authorities. In a joint statement with the senior Tory on the ISC, Michael Mates, Howells said: "The director general has confirmed to us this evening that no document concerning Binyam Mohamed and his treatment by the US authorities has been withheld from us." Any claim that the intelligence services were colluding in torture was "a calumny and a slur and it should not be made".