Revelations that senior officials were informed as long ago as 1991 appear to contradict MoD claims that they only learnt recently of the possible link with "Gulf War Syndrome".
It has also emerged that a team of scientists with acknowledged expertise applied for MoD funds in August to carry out further research - but were turned down by the Medical Research Council without explanation. Nicholas Soames, the defence minister who revealed the possible link with organophosphate pesticides (OPs) on Friday, said details of a major research programme run by the MRC will be announced next month.
Yesterday Michael Portillo, Secretary of State for Defence, said the MRC had set up "the most comprehensive medical investigation" into the issue.
MoD officials said that thousands of troops will be interviewed to see if rules were broken. "We are looking at people who did not follow the standard operating procedures."
Meanwhile the most telling evidence that senior MoD personnel were aware of health hazards from pesticides come in documents prepared by an army health expert and seen by the The Independent. In the documents, Sgt Anthony Worthington, environmental health adviser to 4 Armoured Brigade in the war, says that "at no time" were staff applying insecticides issued with protective clothing, that instructions were sometimes in Arabic, leading to wrong dosages, and that some containers leaked.
Crucially, Sgt Worthington, who is now ill and is seeking compensation, says that two majors were at a meeting in which he complained about the lack of protective equipment.
The report which deals with the leaking containers, marked "restricted" and dated 31 March 1991, is also referred to by a lieutenant-colonel in a separate document. It praises the sergeant and proves that senior officers were aware of at least some of his concerns.
Two other reports to the MoD came in 1995. Hilary Meredith, the solicitor representing Gulf veterans, said she wrote to John Major and Mr Portillo informing them of the Worthington memos.
And last July, Dr Goran Jamal, a consultant at the Institute of Neurological Science at Southern General Hospital, Glasgow, explained to two MoD experts his findings that OPs were an "essential contributor" to the illnesses in soldiers known as Gulf War Syndrome.
Dr Jamal also said his institute and the Institute of Occupational Medicine in Edinburgh had applied to the MRC in August this year for MoD funding for research into the impact of OPs but were turned down.
He believes the symptoms in up to 750 UK troops who have become ill are caused by a mixture of OP poisoning, contamination by nerve-gas agents and the impact of pyrostigmine bromide tablets, issued to protect soldiers from such nerve agents.