Advice on a government website suggests that high-fat, low carbohydrate diets - such as Atkins - may increase the risk of cancer and heart disease.
Low-carbohydrate diets have been criticised
The Food Standards Agency says that high-fat diets are linked to obesity - and "unpalatable and dull".
There is controversy over the health benefits of the Atkins diet - adherents say that it not only achieves rapid weight loss, but at no health cost.
However, officials claims that moderate intake of carbohydrate and fat is best.
Senior FSA nutritionist Sam Church offers the diet advice on the agency's website.
It is the latest in a series of warnings about potential health risks from eating smaller portions of carbohydrates - bread, rice, pasta or potatoes - but as much as you like of high-protein, high-fat items such as cheese, eggs and meat.
An estimated three million people in the UK have at some point tried the Atkins Diet, which was first developed in the 1970s.
The FSA does not mention Atkins by name - in fact her description is of diets which "cut out starchy foods altogether" - not a fully accurate description of the diet plan.
However, Ms Church says: "Cutting out starchy foods, or any food group, can be bad for your health because you could be missing out on a range of nutrients.
"Low-carbohydrate diets tend to be high in fat, too, and eating a diet that is high in fat could increase you chances of developing coronary heart disease."
She adds: "High-fat diets are also associated with obesity, which is currently increasing in the UK.
"People who are obese are more likely to develop conditions such as diabetes and some cancers."
She also claims that low-carb diets tend to be also low in vegetables and fruit - also depriving the body of vital nutrients.
This again, does not precisely match the Atkins approach - after more severe restrictions in the first fortnight, the Atkins diet actually encourages the eating of many types of green vegetables as part of a daily routine.
There is no current evidence linking Atkins directly to any health problems such as cancer, diabetes and heart disease.
Followers of the Atkins diet say that it is frequently misrepresented in print - and in statements from health bodies.
In fact, they say, after the induction phase, the quantity of permitted carbohydrates does begin to rise - although not hugely.
Atkins fans say that despite the restrictions on what they can eat, they have generally ended up eating a far greater variety of fresh foods on the diet compared with normal.
Many dieters said they were obese - and at greater risk of cancer, heart disease and diabetes - prior to starting the diet, and the subsequent weight loss should lessen that risk rather than increase it.