Last night, the Department of Health stressed that on the basis of what is currently known, no one should stop drinking milk. The nationwide survey was ordered after initial tests at 16 dairies in Northern Ireland showed the bacteria - mycobacterium paratuberculosis in around a quarter of the samples taken.
Even treated milk contained the organism although previous research had shown that pasteurisation should be effective in destroying it.
The bacteria has been suggested as a factor in the cause of Crohn's. Symptoms of Crohn's include severe stomach cramps, sickness and diarrhoea, and some cases lead to ulcers and tumours in the bowel and intestines.
There are thought to be more than 80,000 sufferers in this country and 75% of patients will eventually have surgery. There is a slight inherited tendency to develop the disease.
A spokesman for the National Farmers' Union said: "We support any research that gives strength to the argument that milk is a nutritious and wholesome product. We don't believe there is any doubt whatsoever about the safety of milk."
The bacteria is the cause of Johne's disease, a disorder of cattle across the world although cases in Britain are rare according to the NFU.
A spokesman for the Department of Health said: "There is no reason at all at the moment why anyone should reduce their consumption of milk. It has been advised by experts that we carry out this survey after the findings from Northern Ireland. It is an extremely small survey but the prevalence was quite high there. We need to know more about it before we can say any more. A lot of people drink milk and we wish to put people's minds at rest as soon as we can."
The Ministry of Agriculture, Fisheries and Food will examine more than a thousand samples of all types of milk for a range of bacteria. But the Advisory Committee for the Microbiological Safety of Food has asked that samples be tested for this particular strain.
The survey has been adapted to investigate the initial Northern Ireland findings in more depth. In total, 62 samples were collected, 31 of raw milk and 31 of pasteurised milk; provisional results indicated the presence of mycobacterium paratuberculosis in 10 raw milk samples and six pasteurised milk samples.
A spokesman for Maff said: "The advisory committee has examined the issue on a number of occasions and have advised that as yet there is no evidence of a public health problem but that it would nevertheless be prudent to conduct further research and to keep the evidence under review."
Dr Norman Simmons, a member of the committee , last night played down the risk and defended the Government's decision to go public.
"At best, there is no risk at all. At worst, if those people who think it's capable of causing human disease are correct, at worst I have calculated myself that the risk is about one in five million if you drink a glass of milk," he told ITN's News at Ten.