Jonathan Sumption QC wrote a letter to the Appeal Court on Monday after seeing a draft copy of the judgment of the Master of the Rolls (MR), Lord Neuberger.
The QC said the draft would be read as a court statement "that the Security Service does not in fact operate a culture that respects human rights or abjures participation in coercive interrogation techniques".
The version of the MR's decision published today does not contain the passages objected to by the QC, leading to accusations that it has been "watered down".
The Guardian newspaper, which was a party in the case, later said it was "extremely disturbing" that Government lawyers "made a successful last-ditch attempt to get the Master of the Rolls to re-write his judgment, which had already been circulated in draft form".
All sides in the case are now being given an opportunity to make representations over the issue.
The QC warned in his letter that the MR's original observations "are likely to receive more public attention than any other part of the judgments".
The letter went to the clerk to the MR, and the clerks to the Lord Chief Justice Lord Judge and President of the Queen's Bench Division Sir Anthony May.
In their rulings, all three appeal judges rejected a bid by Foreign Secretary David Miliband to block a High Court decision to disclose seven controversial paragraphs they were previously forced to redact from judgments.
The paragraphs dealt with intelligence service information relating to Mr Mohamed's allegations that he was tortured while held by the CIA, with the knowledge of the British security services.
One of the key paragraphs stated that the reported treatment of Mr Mohamed "could readily be contended to be at the very least cruel, inhuman and degrading treatment of Binyam Mohamed by the United States authorities".
In his letter to the judges, Mr Sumption said the MR's draft observations in upholding the High Court decision "go well beyond" anything found by the court.
The QC said those observations constituted "an exceptionally damaging criticism of the good faith of the Security Service as a whole".
The QC said the MR's suggestion in his draft ruling that the court "should distrust any Government assurance based on the Service's advice and information" would unquestionably be cited in other cases.
If widely applied it would "mark an unprecedented breakdown in relations between the courts and the executive" in the area where the Government relied on public interest immunity.
Mr Sumption said there was insufficient material to justify the MR's findings.
The Security Service "has received no notice whatever of the court's intention to make such sweeping criticisms".
The QC referred in particular to paragraph 168 of the MR's draft judgment.
He said the MR had made statements that would be read as meaning that "officials of the Service deliberately misled the Intelligence and Security Committee" in a way that "reflects a culture of suppression in its dealings with the Committee, the Foreign Secretary and indirectly the court".
They would be read as saying that the culture of suppression "penetrates the Service to such a degree as to undermine any UK Government assurances based on the Service's information and advice".
Also that the Service "has an interest in suppressing information which is shared, not by the Foreign Secretary himself (whose good faith is accepted), but by the Foreign Office for which he is responsible".
Mr Sumption said that "reads like an accusation of bad faith against those FO officials who have advised the Foreign Secretary".
The QC ended his letter: "I respectfully invite the Court to reconsider whether paragraph 168 is necessary to its decision, and whether it really does justice to those involved".
Later the Guardian said in a statement: "It is good news that - after challenge from the Guardian and other news organisations - the courts have finally ordered the government to reveal evidence of MI5 complicity in torture.
"This is a watershed in open justice in an area where it is notoriously difficult to shine a light.
"But it was extremely disturbing that the government's lawyers made a successful last-ditch attempt to get the Master of the Rolls to re-write his judgment, which had already been circulated in draft form.
"There are now effectively two judgments. The one released today is a watered down version of the original judgment - diluted at the request of the government, via its leading counsel, Jonathan Sumption QC.
"A crucial passage has been removed.
"The Guardian and Liberty intervened (on Tuesday) night to express their concern at what had happened.
"It is good that the Master of the Rolls has agreed to reconsider his decision to re-write his judgment in response to Government representations."
Media lawyer Mark Stephens said: "It is a breach of the long-standing constitutional principle (from the 1637 Ship Money case) that governments may not secretly communicate with the court or with judges."
Later, a Foreign Office spokeman said: "This is not about suppressing criticism of the agencies.
"This is about ensuring the judgment did not contain unsubstantiated allegations that could have prejudiced ongoing legal proceedings.
"Let us be clear that the content of the final judgment was a matter for the court.
"The final judgment has been published and therefore that version is the view of the court, not working drafts."
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