I testified last week to the Chilcot inquiry. My experience demonstrates an emerging and dangerous problem with the process. This is not so much a problem with Sir John Chilcot and his panel, but rather with the government bureaucracy – Britain's own "deep state" – that is covering up its mistakes and denying access to critical documents.

There is only one solution to this problem, and it requires decisive action.

After I was invited to testify, I was contacted by the Foreign Office, from which I had resigned after giving testimony to the Butler inquiry in 2004, to offer its support for my appearance. I asked for access to all the documents I had worked on as Britain's Iraq "expert" at the UN Security Council, including intelligence assessments, records of discussions with the US, and the long paper trail on the WMD dossier.

Large files were sent to me to peruse at the UK mission to the UN. However, long hours spent reviewing the files revealed that most of the key documents I had asked for were not there.

In my testimony I had planned to detail how the UK government failed to consider, let alone implement, available alternatives to military action. To support this 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, thereby sustaining the Saddam 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.

I had also asked for all the Joint Intelligence Committee assessments on Iraq, some of which I helped prepare. Of dozens of these documents, only three were provided to me – 40 minutes before I was due to appear before the Chilcot panel.

Playing by the rules, I had submitted my written testimony to Chilcot before my appearance. In the hours before my appearance, invited to visit the Foreign Office to see further documents (mostly irrelevant), an official repeatedly sought to persuade me to delete references to certain documents in my testimony.

He told me that the Cabinet Office wanted the removal of a critical reference in my evidence to a memo from a senior Foreign Office official to the foreign secretary's special adviser, in which the official pointed out, with mandarin understatement, that the paper sent that week to the Parliamentary Labour Party dramatically – and inaccurately – altered the UK's assessment of Iraq's nuclear threat.

In a clear example of the exaggeration of Iraq's military capabilities, that paper claimed that if Iraq's programmes remained unchecked, it could develop a nuclear device within five years.

The official's memo pointed out that this was not, in fact, the UK assessment: the UK believed that Iraq's nuclear programme had been checked by sanctions.

The paper to the PLP was instead sent by the foreign secretary to "brief" the wider cabinet. This paper was pure overstated propaganda, filled with ludicrous statements like "one teaspoon of anthrax can kill a million people". The paper was soon made public, as part of the campaign to create public hysteria.

The official's memo about the PLP paper contained nothing secret. It relates to a public document, the PLP paper. Yet, of all the references in my testimony, this was the one that the Cabinet Office most wanted removed. I refused. Strikingly, this memo has never been mentioned to the inquiry, including by its author, who testified earlier this year. Neither has the author of the PLP paper been questioned, or the paper itself discussed.

I was repeatedly warned by inquiry staff not to mention any classified material during my testimony. The only problem is that almost every document I ever wrote or read in my work was classified. It was made clear to me, and to journalists attending the hearing, that if I mentioned specific documents the broadcast of my testimony would be cut off. Other forms of retribution (Official Secrets Act prosecution?) hung in the air. It was a form of subtle intimidation.

Meanwhile, my requests to see documents about the infamous Number 10 WMD dossier were ignored, including requests for letters I had written.

This experience and the inquiry's record so far is cause for concern. It is clear from testimonies so far that most witnesses, most of whom went along with the war at the time, are offering a very one-sided account to the panel. A story is being peddled that sanctions on Iraq were collapsing and the allied policy of containment was failing. Thus, the military alternative to deal with the Iraqi threat was more or less unavoidable.

Though there is some truth to this argument, it was not what the Foreign Office, or the government as a whole, believed at the time. The true story is there to be seen in the documents. In memos, submissions to ministers and telegrams, the official view is very clear: while there was concern at the erosion of sanctions, containment had prevented Iraq from rearmament.

When invasion was promoted by Washington, the available alternative – to squeeze Saddam financially by stopping oil exports or seizing the regime's assets, which I and some colleagues had repeatedlyadvocated, was ignored. Here the documents tell a different but equally clear and appalling story: there is not a single mention of any formal discussion, by ministers or officials, of alternatives to military action. It is hard to pinpoint a graver indictment of the government's failure.

The oral testimonies delivered to the inquiry have not given an accurate picture of what the government really thought. Unfortunately, the panel is neither equipped, nor apparently inclined, to challenge witnesses on the contradictions of their testimonies with this documentary record. This may not be the panel's fault: how can they know which pertinent documents exist?

In these circumstances, 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 – and documents. I have been told too, from secondary sources, that members of the panel have been refused documents they have specifically requested.

There is a clear solution to these problems: break down the continued obstruction by the bureaucracy by releasing the documents – all of them. Only the most secret documents deserve continued protection, and there are very few of these. The vast majority of relevant documents relate to policy discussion inside the government before the war. Though profoundly embarrassing, there is little here that damages national security, except in the hysterical assessment of officials protecting their own reputation. Nick Clegg said a few weeks ago that almost all documents must now be released. He is right.

Carne Ross was the UK's Iraq expert at the UN from 1997 to 2002. He now heads Independent Diplomat, a non-profit diplomatic advisory group.