The ruling led to the release of a seven-paragraph summary of 42 classified CIA documents that were handed to MI5.
They show that MI5 was aware that Mr Mohamed was being continuously deprived of sleep, threatened with rendition and being subjected to "significant mental stress and suffering".
After seeing a draft version of Lord Neuberger's judgment - particularly paragraph 168 - Government lawyers took the view that he had unjustifiably gone further in his criticism than the other two judges.
Jonathan Sumption QC, wrote to the court on the Government's behalf warning that Lord Neuberger would be seen as saying the Security Service did not respect human rights and had failed to renounce participating in "coercive interrogation" techniques.
In his letter to the judges, Mr Sumption said Lord Neuberger's draft observations in backing the High Court decision went "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 suggestion 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 Government.
Mr Sumption said the Security Service "received no notice whatever of the court's intention to make such sweeping criticisms".
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