Coverage had 'unfairly damaged' the system of government and the reputation of the civil service, he said.
Sir Robin made his attack in a prepared statement read out to the inquiry. He said he was supported by the head of the diplomatic service, Sir David Gillmore. A spokesman said the Prime Minister was aware of and had not objected to Sir Robin's proposal.
His statement emphasised that the task of civil servants giving evidence to the inquiry had been made 'more fraught and onerous by grossly distorted and prejudicial allegations in the media about the role of government and individuals, including civil servants, in these matters.
'While I make no criticism or complaint about the inquiry's procedures, the absence of the restraints on comment about the course of the proceedings which would apply in a court of law has permitted wild allegations and prejudging of issues in media reports.'
He complained about the way the inquiry, which is investigating the sales of millions of pounds of British defence-related exports to Iraq, was referred to as the 'arms-to-Iraq inquiry'. The Government had not authorised any weapons for export to Baghdad, he said.
He also attacked references to public interest immunity certificates, signed by ministers seeking to suppress government documents from the Matrix Churchill trial, as 'gagging orders'.
Referring to 'scrapbook items', he cited headlines about himself including: 'The Butler did it'; 'Cabinet chief linked to Iraqi gun cover- up' and 'The trail of blood running through Whitehall in the wake of the arms-to-Iraq affair leads to the door of the Cabinet Secretary' as examples of coverage.
Sir Robin also revealed prosecution lawyers and investigators in the Matrix Churchill case did not see the Cabinet Office papers until October 1992, the month the trial began and two years after the defendants were first charged.
Presiley Baxendale QC, the inquiry counsel, said: 'If Customs were to get a full picture of what was going on, surely something like these documents relating to a meeting between Mr Clark and the Prime Minister must count as something relevant Customs should see?'
Sir Robin said there had been no intention to release the documents to the court unless there was a successful application by the defence. He said that they were not 'crucial' to the case.
He also defended a decision to block two retired Ministry of Defence officials giving evidence to the House of Commons Trade and Industry Select Committee supergun inquiry in 1992.
Sir Robin said it was an 'established practice' that only serving officials gave evidence to Commons select committees. He claimed because ministers 'ultimately take the rap' they had a right to choose who represented them before MPs.
He also said he ordered a review of the distribution of intelligence within Whitehall following revelations at the inquiry that vital information from Britain's intelligence agencies was not being passed to relevant officials or ministers.
Sir Robin said that although select committees could force someone to appear before them, a minister could order an official, serving or retired, to refuse to answer.
Lord Justice Scott suggested that if ministers' powers to do that were ever tested in court 'I would have assumed such an arbitary use of confidentiality would not be upheld'. Sir Robin replied this was probably the reason that the Government and Parliament were anxious such matters were not dealt with by the courts.