Lord Justice Scott said Jordan's absence left a 'glaring loophole' in attempts to stop exports of chemical and biological warfare weapons to Iraq.
The 'countries of concern' list was drawn up in 1991 to help exporters identify countries they should avoid supplying with products used to make chemical, biological or nuclear weapons.
Peter Vereker, head of the Foreign Office Arms Control and Disarmament Department (ACDD), told the inquiry that Douglas Hogg, a Foreign Office minister, wanted Jordan included on the list after reading Germany's equivalent list.
But another Foreign Office department responsible for Jordan challenged this.
The disagreement was referred to a special Cabinet Office meeting for a decision. Before it had met, a letter containing a proposed list of countries had been sent for approval to the Prime Minister's office by Peter Lilley, then Secretary of State for Trade and Industry, without Jordan on it.
Lord Justice Scott said he found it hard to understand how officials could challenge a decision made by a Foreign Office minister. Presiley Baxendale QC, inquiry counsel, said it was 'astonishing' that Mr Hogg was not told what had happened.
The inquiry heard a senior official on learning of the omission, wrote on a memo: 'Jordan's disappeared. Well done.'
Mr Vereker said he did not share the same 'congratulatory peal of triumph', but did nothing since the priority was to get the list published.
He said that better methods of preventing proliferation were consulting intelligence agencies, lists of prohibited goods and export licence applications.
But Whitehall documents written in July 1992 revealed that Mr Vereker's department was no longer interested in checking potential warfare export licence applications to Jordan although defence experts scrutinised them because there was a 'high potential Jordan was a diverter proliferator'.
Asked why it was not important to see the licences, given recent doubts about Jordan, Mr Vereker failed to give a full answer. Pressed by Lord Justice Scott, Mr Vereker said he did not know of any evidence of diversion from Jordan.
The inquiry heard that a civil service brief to Tim Sainsbury, the Industry minister, to help him answer a question from a member of the public about why Jordan was omitted from the list, claimed its inclusion was 'not merited'. Asked by Lord Justice Scott if this was 'simply not true' because Jordan had only been left out while the inclusion was challenged, Mr Vereker said that he found the claim 'surprising' and 'misleading'.Reuse content