Jeff Rooker, the food safety minister said he had accepted advice from the independent Food Advisory Committee (FAC) that the level of the vitamin should be limited to 10 milligrams per daily dose sold over the counter.
Mr Rooker said: "Vitamin B6 is an essential component of people's diets. But like many things, too much can be harmful." Legislation would be introduced to control the products, he said.
Experts have warned prolonged exposure to high levels of the vitamin could cause damage to the nerves leading to numbness, clumsiness and tingling.
But critics claimed that the proposed 10 milligram daily dose was "ridiculously low" and a blow to thousands of women using doses of up to 200mg a day to combat pre-menstrual syndrome and depression.
The new controls mean that high dose pills up to 50mg may only be sold under the supervision of a pharmacist and above 50mg the pills will be available only on prescription.
In future, all pills will have to carry a warning label about the risks of exceeding a 10mg a day dose.
High-dose supplements currently on sale are not being withdrawn, but manufacturers are being urged to voluntarily print warning labels on the packaging until the legislation comes into effect.
The Royal Pharmaceutical Society yesterday advised pharmacists to remove the high-dose pills from open sale immediately and treat them as "pharmacy only" medicines so that customers can be told of the risks.
John Ferguson, secretary of the society, said: "The health department has stressed that the health risks associated with higher doses of vitamin B6 are low. However, as pharmacists our primary concern is the safety of the public."
Vitamin B6 is found in a wide variety of foods including cereals, potatoes, milk, meat and beer.
The Ministry of Agriculture said surveys showed that the average intake of the vitamin from the diet at 2mg a day is "more than sufficient to maintain health".
Most dietary supplements already comply with the 10mg dose limit which is still five times the recommended daily dose. Sue Croft, of Consumer for Health Choice lobby group, said the government action flew in the face of the bulk of research showing it was safe to take up to 200mg a day.
She said: "The level being proposed is ridiculously low.
"For some women, 10mg is no good at all, they need a much higher level of nutrients to combat symptoms of pre-menstrual syndrome such as irritability and water retention."
The health food chain Holland & Barrett said it was still quantifying how many products would be affected.
A spokeswoman said: "It is going to be a considerable number of products and so a considerable number of customers.
"I don't think women using the higher dose supplements or their doctors are going to be too happy if they become prescription only."
But Sue Todd, of the Consumers' Association, which campaigned for the review, welcomed the move and said it was a shame manufacturers had not voluntarily reduced levels of the vitamin following an initial recommendation by the FAC last year.Reuse content