Seasonal Canine Illness is linked to the bites of bharvest mite larvae, they believe.
Of 95 cases of the illness between September and October this year in five surrounding areas, 49 were linked to the royal estate in Norfolk, making it the worst affected part of the country.
Two dogs which were walked on public land there have died from symptoms including vomiting, diarrhoea and lethargy this year.
Last year 37 dogs were diagnosed with the illness after visiting Sandringham and six died. Harvest mite larvae are the size of a pinhead and occur naturally in woodland and fields at the end of the summer and in the autumn.
But the Animal Health Trust, which investigated the outbreaks, says no new cases have been reported for at least a month.
The estate has put up warning signs.
The Queen is believed to have welcomed the news as it means her beloved corgis and labrador gun dogs will not be at risk during her Christmas and New Year break.
Natural History Museum botanist Dr Mark Spencer suffered an infestation of harvest mite bites on his own leg after walking through undergrowth on the estate.
Further research is now being carried out to establish how the mites, which normally only cause a mild irritation to mammals, might have passed on serious illness to dogs.
A spokeswoman for Buckingham Palace said: “The Sandringham estate is taking the reports of sick dogs very seriously. The estate has been taking steps to warn people.”