Former soldiers who served in the conflict have told The Independent they believe that camels, sheep and domestic animals which died in the war were killed by pesticides.
Army chiefs ordered that the animal corpses be sent back to the UK for scientific tests to determine the cause of their deaths.
Last July, in response to a Parliamentary question, Earl Howe told Parliament the experiments at an Edinburgh veterinary centre had shown the animals died of natural causes.
But last night, after inquiries by The Independent and Granada Television, the director of the Centre for Tropical Veterinary Medicine in Edinburgh, which Earl Howe said carried out the tests, said he had no record of such work ever being done.
Professor David Taylor said staff at the centre had no recollection of such tests. He has written to Earl Howe asking for an explanation of the information given to Parliament last July.
"I have gone back through all our computerised records, and we have no record of ever having done this work."
He added: "I have written to Earl Howe and asked him if he could let me know exactly who received these sample because we are at a loss to know where this information in Hansard comes from."
The MoD said it had begun an internal inquiry into how the minister had been misinformed.
A spokesman said: "We are getting all the paperwork out to see who advised the minister in his reply. Perhaps there is confusion in the name of the learned body [which did the experiments]. It seems clearly to have not been the Centre for Tropical Veterinary Medicine."
Last July the Countess of Mar, who has taken a special interest in the effects of organophosphate insecticides and other chemicals on British troops, asked whether the animals had been exposed to nerve gas.
In his reply Earl Howe said: "Samples from dead animals were sent back to the Edinburgh Veterinary School and Tropical Medicine Centre [sic] and all were found to have died of natural causes or such things as eating vehicle batteries."
At the time the answer was given, the MoD was denying the use of organophosphate insecticides (ops) in the Gulf War.
Three months later, Nicholas Soames, the Armed Forces minister, apologised to the House and said he had been misinformed: ops had been used to protect troops from desert pests.
Yesterday, troops who served in the conflict told of how they were ordered to put the animal carcasses into plastic bags to be flown back to Britain.
Cpl Richie Turnbull, a Chester-based RAF veteran, said: "All the flies on the animals were dead as well. It was very strange." He said that he was sure that the dead animals were being sent back to military labs.
Sgt Angus Parker, a laboratory technician who was working for scientists from the Porton Down chemical and biological defence establishment in Wiltshire, attributes the animal deaths to the use of pesticides.
He said he accompanied body-bags containing animals as they were flown to Boscombe Down, the military airport in Wiltshire, close to Porton Down. "They were taken away in lorries and I am pretty sure they were not going to Scotland," he added.Reuse content