The criticisms, contained in a statement for which Lord Justice Scott and his staff were clearly unprepared, came at the opening of his evidence to the inquiry.
The former Foreign Secretary attacked Lord Justice Scott for failing to follow the six principles laid down by the 1965 Salmon Royal Commission report into the conduct of inquiries.
He said witnesses were not being given advance notice of any allegations, and had no chance of having their own legal representation or stating their own case in public.
The findings of the Scott inquiry could be dismissed, he warned, because the Salmon principles of fairness were not being followed. Witnesses and observers were 'anxious'. Lord Howe said the judge and his team were acting as 'detective, inquisitor, advocate and judge' which meant not all the 'safeguards regarded as habitual' were being enjoyed.
When Lord Howe said some witnesses felt anxious, the judge retorted: 'It would perhaps be better if they had expressed that to me.' Lord Howe refused to reveal to whom he was referring when challenged by the judge, and suggested the judge would have benefited from the advice of lay assessors.
Lord Howe said his comments were prompted out of concern for the reputation and morale of his former 'flock' of officials, diplomats and MI6 officers who had served him and Britain 'loyally and with great diligence' while Foreign Secretary.
'At all times, they were doing their personal best to perform their duties to the utmost of their ability and by and large, they achieved or exceeded standards' set elsewhere. Britain's diplomatic service was the best in the world, he said.
Angered by Lord Howe's outburst, Lord Justice Scott moved swiftly to reject the accusations which were described as a 'bolt out of the blue'. Christopher Muttukumaru, the inquiry secretary, said in a statement authorised by the judge, it would have been 'ludicrous' to allow each witness or department to be legally represented, although legal assistance was available to anyone seeking it.
Mr Muttukumaru said: 'Lord Howe was asked by the judge to identify those for whom he was speaking. He would not do so. If he is speaking on behalf of the Foreign Office, or the Government more generally, I should say no complaint has been made to the inquiry about its procedures by either.'
Lord Justice Scott said he did not regard the Salmon recommendations as a blueprint for every inquiry, and said had they been followed, it would have postponed his report 'by a number of years'.
He said the inquiry procedures were designed to achieve fairness to every witness and had been agreed after consultation with government departments and 'interested individuals'. Not a single witness had complained directly, he said.
Witnesses knew what they were to be questioned about before appearing as they were sent detailed questionnaires beforehand.
Leading article, page 19