Animal feed manufacturer Dodson & Horrell is holding a full investigation into how possible component contamination could have occurred after Estimate, owned by The Queen, tested positive for morphine.
Dodson & Horrell, horse and dog food manufacturer to The Queen since 2006, identified Alfalfa Oil Plus as the possible product which had been contaminated.
The company said it has launched a "thorough investigation" with its unnamed supplier of a component.
Dodson & Horrell believes contamination could have occurred from poppy seeds that occur naturally in the environment.
Initial indications are that the positive test taken from Estimate, the 2013 Ascot Gold Cup winner, resulted from the consumption of a contaminated feed product, Buckingham Palace said in statement on Tuesday evening.
The Palace said Her Majesty has been informed of the development.
A statement issued on behalf of Dodson & Horrell said: "Preliminary investigations suggest that any contamination of this component product did not occur at Dodson & Horrell's site.
"The investigation is currently centring on Dodson & Horrell's supplier.
"Dodson & Horrell has recalled batch numbers week 20-28 of Alfalfa Oil Plus as a precautionary measure, in accordance with our procedures and NOPS (naturally occurring prohibited substances) protocol.
"No positive test results have been recorded in any other Dodson & Horrell product currently in the market.
"From information currently available to us, it appears that any contamination may have come from poppy seeds that occur naturally in the environment. Please note this does not affect the welfare of the animal.
"Investigations are ongoing through the official and correct channels. Information will be shared by Dodson & Horrell as it becomes available."
Estimate, trained in Newmarket by Sir Michael Stoute, produced one of the headline stories of last season with a nail-biting triumph in the Gold Cup at the Royal meeting.
She then went down narrowly to Leading Light in the defence of her crown last month.
The five-year-old mare is reportedly still in contention for the Artemis Goodwood Cup next Thursday and worked on Wednesday morning over nine furlongs in Newmarket alongside stablemates Snow Sky and Top Tug.
The British Horseracing Authority announced last week that five horses under the care of various trainers have been reported to show the presence of morphine in their 'A' samples.
"Once all processes have been completed, the cases will be put before a disciplinary panel who will decide what action, if any, should be taken," said a BHA statement last Thursday.
"This may include the disqualification of the horses in question from the relevant races."
Lambourn trainer Charlie Hills is reportedly one of the other trainers who has had a horse test positive for morphine.