Public concern would be 'impossible to allay' if material was unnecessarily kept secret, his inquiry team said.
The warning came at a meeting last week between Christopher Muttukumaru, the inquiry secretary, and representatives from the Whitehall departments involved, details of which have only just been revealed.
Mr Muttukumaru said: 'I hope that witnesses and Whitehall will be under no illusion about the extent to which the judge is determined, subject to safeguards, to make available as much information as he can.
'This inquiry was established because of public concern about the way in which the Government policy operated in relation to defence and defence-related sales to Iraq.'
He added: 'It would be impossible to allay public concern if material were unnecessarily withheld from publication.'
Lord Justice Scott has said that he will consider special requests to keep information confidential, particularly where disclosure was not in the national interest, put individuals in danger or seriously prejudice legal proceedings.
He has also said that pleas to protect documents should only be made in 'the clearest of cases'.
Mr Muttukumaru, spelling out the judge's timetable, said that Lord Justice Scott hoped to complete the first draft of the report by the end of July.
Witnesses criticised in the report would be given an opportunity to comment during August and September, with the intention of publishing his final report 'towards the end of the year'.
The inquiry team still believes that a number of questions remain unanswered and written requests for more information would be sent out, Mr Muttukumaru added.
One question Lord Justice Scott is seeking an answer to is whether government departments, criticised for failing to give Customs important documents relevant to the Matrix Churchill prosecution early enough, did so because they did not make sufficient resources available.
Among the witnesses who will give evidence to the inquiry next month is Sir Brian Unwin, the former chairman of Customs.