A key witness to the Chilcot inquiry into the Iraq war has accused Whitehall of trying to silence embarrassing testimony undermining the case for the invasion.

In today's Observer, Carne Ross, the UK's Iraq expert at the UN between 1997 and 2002, writes that the inquiry is being prevented by "deep state" forces from establishing the government's true motivation for invading Iraq.

Ross, who appeared before the inquiry this month, says he was not provided with key documents relevant to his testimony and was warned by officials not to refer to an internal Foreign Office memo that contradicted the government's public case for war.

Before his appearance, large files were sent to him to read in confidence at the UK mission to the UN in New York, but "most of the key documents I had asked for were not there". In the hours before his appearance, Ross visited the Foreign Office, where he says "an official repeatedly sought to persuade me to delete references to certain documents in my testimony".

Ross claims he was told his evidence must not refer to a memo from a senior Foreign Office official. The memo, to the special adviser to the then foreign secretary, Jack Straw, expressed concern that a briefing paper for the parliamentary Labour party had "dramatically" altered the assessment of Iraq's nuclear threat. Ross says the "paper claimed that if Iraq's programmes remained unchecked, it could develop a workable nuclear device within five years. The official's memo pointed out that this was not in fact the UK assessment, which was more or less the opposite: that the UK believed that Iraq's nuclear programme had been effectively checked by sanctions."

Despite the official's concern, the paper was used to brief the cabinet. Ross writes: "This paper was pure overstated propaganda, filled with almost ludicrous statements like 'one teaspoon of anthrax can kill a million people'."

He expressed incredulity that the Foreign Office wanted references to the briefing removed from his testimony, as it related to a public document. "It is very worrying that the government machine is still trying to withhold key documents, and silence those of us with detailed knowledge of the policy history. I have been told too... that members of the [inquiry] panel have been refused documents they have specifically requested."

Simon Hughes, the Liberal Democrat deputy leader, said: "The Chilcot inquiry will not be credible if relevant documents that do not now threaten national security are kept from the inquiry and the public."

Ross said he had wanted to use his appearance to highlight how ministers failed to consider alternatives to military action. "I had asked for specific records relating to the UK's failure to deal with the so-called Syrian pipeline, through which Iraq illegally exported oil, sustaining the Saddam [Hussein] regime. I was told that specific documents, such as the records of prime minister [Tony] Blair's visit to Syria, could not be found. This is simply not plausible." He also asked for joint intelligence committee assessments on Iraq, some of which he helped prepare and all of which he had seen. "Only three were provided – 40 minutes before I was due before the Chilcot panel."

The claims come at the end of a week in which the former head of MI5, Dame Eliza Manningham-Buller, cast grave doubts on the case for invading Iraq and the deputy prime minister, Nick Clegg, described the invasion as "illegal".

A Cabinet Office spokesman said the inquiry was committed to being fair to all witnesses. "The inquiry wrote to Mr Ross four weeks prior to his appearance, highlighting that if he wished to refer to any specific documents he should notify the Iraq inquiry secretariat in advance so they could seek any necessary declassification. As Sir John Chilcot highlighted, Mr Ross did not ask in advance for any documents to be declassified."