All flour is to be fortified with folic acid after ministers swung behind a plan that medical experts say will reduce the number of babies born in the UK with serious birth defects, the Guardian can reveal.

The policy, which will be introduced within weeks, comes after ministers were convinced by their own advisers that it would reduce the risk of babies developing spina bifida and other conditions that involve severe disability or death.

Until now, ministers in successive governments have ignored repeated pleas to embrace mandatory folic fortification.

Downing Street has approved the switch after a long-running campaign by doctors, scientists and baby health campaigners, well-placed Whitehall sources say. Theresa May, who was opposed, has been persuaded to change her mind, a key official said.

Medical groups and health charities welcomed the decision.

“Mandatory fortification will be a game-changer for the UK,” said Kate Steele, the chief executive of the charity Shine, which helps families affected by neural tube (birth) defects.

“A government decision to introduce mandatory fortification will mean a major positive impact for the health and wellbeing of babies born in the future. In many cases, it will be the difference between life and death.”

A host of government, NHS and advisory bodies support fortification, which already happens in more than 80 countries, including the US.

The move is also backed by medical royal colleges, including those representing professionals involved in babies’ and children’s health – obstetricians and gynaecologists, paediatricians and midwives. In the US there has been an estimated 23% reduction in neural tube defects (NTD) since folic fortification of flour was introduce in 1998.

Taking enough folic acid in pregnancy is estimated to reduce by as much as 70% the risk of a NTD such as anencephaly, a fatal condition in which the foetus develops without a major portion of the brain, skull and scalp and dies in utero or shortly after birth.

It is estimated that two women a day in the UK have an abortion because doctors have identified an NTD and two children a week are born with an NTD, often spina bifida, which in some cases can necessitate the use of a wheelchair.

Britain is believed to have the highest rate of NTDs in Europe. A major academic study in 2015 estimated that 2,000 fewer babies in Britain would have been born with an NTD between 1998 and 2015 if the government had introduced folic fortification of flour.

Until now women in the UK who are pregnant or are hoping to have a child are advised to take folic acid supplements to increase their intake of folate, an approach the Royal College of Obstetricians and Gynaecologists (RCOG) says is ineffective.

Official advice is a daily supplement of 400 micrograms of folic acid when trying to become pregnant and up until the 12th week of pregancy. But many women, especially those in poorer homes, do not take enough.

Dan Poulter, a Conservative MP and former health minister who is also an NHS doctor, praised the government for having finally deciding to introduced mandatory fortification of flour.

“It is good to see that medical evidence has prevailed over political considerations and that the health of mothers and their babies has overcome the previously successful attempts by vested business interests complaining to government about the regulatory and cost burden to businesses. The lives and health of babies is what matters.”

Steve Brine, the public health minister at the Department of Health and Social Care (DHSC), has been pushing the case for fortification in Whitehall. Public Health England has recently made clear to ministers that the move would be a significant step towards improving babies’ health.

Labour’s Owen Smith and Lord Rooker, a former chair of the Food Standards Agency, have also been lobbying ministers. So has the DUP’s Nigel Dodds, whose son Andrew had spina bifida and hydrocephalus. Andrew died aged nine in 1998.

A study published in January was widely accepted as disproving the concern that fortification risked people consuming more than 1 milligram of folate a day, which could of itself be dangerous. The committee on toxicology of chemicals in food, consumer products and the environment, which advises the FSA, has been analysing the issue and is due to report soon, after which ministers are likely to unveil the fortification policy.

Dr Alison Tedstone, chief nutritionist at PHE, said: “Three-quarters of 16- to 49-year-old women have folic acid levels below the new World Health Organization recommendation for women entering pregnancy. Fortifying flour with folic acid is an effective and safe measure to reduce the number of pregnancies affected by neural tube defects.”

Prof Lesley Regan, the president of the RCOG, said it “would welcome the introduction of mandatory fortification across the UK with the appropriate safeguards, such as controls on voluntary fortification by the food industry and improved guidance on supplement use”.

Anne Heughan, a board member at the Royal Society for Public Health, said: “This public health measure of fortification is long overdue and would bring the UK in line with many other countries.”

A DHSC spokesperson said: “Ministers are considering expert advice and will respond in due course.”