It was the clearest sign yet that his final report is likely to contain strong criticism of the Government's use of Public Interest Immunity (PII) certificates.
He cast doubt on whether they were justified in order to safeguard frank advice from officials to ministers and protect government from 'captious and ill-informed and political criticism'.
'The notion that that sort of interest could prevail over the interests of justice in a criminal case has no historical provenance,' he said.
His comments add to the pressure on Sir Nicholas Lyell, the Attorney General, already under fire for advising ministers they had a legal duty to sign the certificates.
The judge also undermined arguments used by other ministers who claimed their duty to protect government papers dated back many decades. He questioned whether a vast range of 'relatively mundane communications between officials and ministers', which the Matrix Churchill defendants said would prove their innocence, were the 'proper subject for a Public Interest Immunity certificate claim'.
Lord Justice Scott said the importance of disclosing the papers to the defence was 'so strong as to make it unthinkable that anybody should use PII to cover documents, of which no more could be said, than that they were confidential'.
His outspoken criticism came after Gerald Hosker QC, the Treasury Solicitor, appearing before the inquiry for a second day, argued that ministers must sign certificates to protect confidential documents if they fell into an established class for which PII had to be claimed.
Mr Hosker said ministers had to satisfy themselves whether documents fell into established classes. Those unhappy at signing could consult with government legal advisers and the prosecuting counsel.
Asked why ministers, as 'guardians of the public interest', should not be able to decide for themselves whether a PII was appropriate, Mr Hosker replied: 'You are introducing the possibility of ministers picking and choosing when PII procedures are followed and when they are not. As an officer of the court, I would not support that at all.'
He said the aphorism 'officials advise, ministers decide' did not apply in this case.
Mr Hosker, praised by the judge for his evidence, admitted Whitehall may not have applied the 'law of PII strictly enough' when asked whether government lawyers had 'cast the net more widely than proper practice requires'.
A new manual advising Whitehall legal departments about PII use was being drawn up, he revealed.
He said he had insufficient detailed knowledge to answer questions from Presiley Baxendale QC, the inquiry counsel, about cases where PIIs were used inconsistently. She said these included Kenneth Clarke's decision to permit an MI6 officer to appear for the prosecution at the Matrix Churchill case, even though intelligence material was normally kept secret. And an MI5 officer also gave evidence for the prosecution, without ministers even being informed.
A further example included a key government document, normally protected by PII, given to the defence when Clive Ponting, a senior civil servant, was prosecuted in 1985 under the Official Secrets Act.Reuse content