Dairy farmers will have to follow tough new rules designed to control an infectious bug which may be spreading from cows to humans through milk.

The bug, commonly found in livestock, can survive pasteurisation and a researcher in the field said it was "inconceivable" that it was not linked to Crohn's disease, a debilitating intestinal condition suffered by about 100,000 Britons.

Research by John Hermon-Taylor at St George's hospital medical school, London, suggests as many as 90% of patients with Crohn's have the bug, mycobacterium avium paratuberculosis (MAP).

"In the light of the new data becoming available, the Department of Health can no longer ignore the strength of the scientific evidence," Professor Hermon-Taylor said.

The government insists that "such a link ... has not been proved nor disproved," but is adopting a precautionary approach to limit the cattle disease, Johne's, which is caused by MAP. It also says action will improve milk yields and reduce culling of livestock. Estimates of MAP infection vary, but a survey has suggested that 17.5% of herds may include infected animals.

Guidance to be issued by the environment department in June will tell farmers to screen herds for Johne's disease, prevent infection through contaminated watercourses and pastures, and protect young calves which may catch it from their mothers and then take years to develop the wasting condition.

Johne's is a difficult disease to control. Because there is a gap of years between infection and the first signs of the disease, it takes farmers a long time to reduce infection.

Prof Hermon-Taylor said the government measures were "prudent" but other changes were needed, including improving surveillance for Crohn's disease by making it compulsory for doctors to report it to health authorities. Only then would it become evident whether farm hygiene measures were having an impact on Crohn's.

Symptoms of Crohn's include diarrhoea, abdominal pain, weight loss and fatigue.