A U.S. Women's Health Initiative (WHI) study was halted three years early in 2002 following such fears. But the then findings were grossly misplaced, says Dr John Stevenson, HRT expert at London's Royal Brompton Hospital.
HRT is normally prescribed to menopausal women in their 50s to combat symptoms such as hot flushes and mood changes, although it also protects bones.
But the WHI study also gave HRT to women in their 60s and 70s, who had gone through the menopause years earlier, with the average age of subject in the research being 63.
The WHI conclusions were overturned last year when re-analysis of the data found the extra risks may apply only to these older patients, who do not normally use HRT.
In fact, hormone therapy was shown to cut heart attacks in women in their 50s.
It did not raise their risk of strokes and they had fewer dangerous calcium deposits in their arteries. Such women had a lower risk of death from any cause compared with those not taking HRT.
A recent study published in the British Medical Journal's Online First edition found that even in women well past the menopause, with no hot flushes, the treatment produced a marked improvement in sleep, sex drive and joint pain.
In May the International Menopause Society issued a review showing HRT is safe and effective for women aged 50 to 59 in the early years of the menopause.
Contrary to 'misperceptions' it does not raise the risk of heart disease for these women and its impact on breast cancer is 'minimal', the panel of 40 international experts said.
Dr Stevenson said he hoped the review had changed attitudes to HRT among women who were missing out and among GPs who had become uncertain about its benefits.
He added: 'I hope that we will be able to restore the confidence in GPs about HRT so that they will prescribe it.'
Women don't know what they are missing out, he says and stresses, 'There is nothing else that is nearly as effective as HRT....It is one of the cheapest treatments we use in medicine and I wonder what the cost to the NHS will be of all the future heart attacks and fractures because of women not having HRT.'
'Women now coming into the menopause are too scared to go on to HRT and I think it is a disgrace,' said Dr Stevenson, who is chairman of the charity Women's Health Concern.
'It has been a huge catastrophe for women and women's health and there is no doubt that women have suffered unnecessarily because of this.'
The number of prescriptions for HRT has fallen from 6.2million in 2001 to a predicted 2.6million for this year as a result of alarming research findings.
In the first five months of this year alone, there were 18 per cent fewer prescriptions compared with the previous year.
He warned that the NHS faces a long-term rise in female patients with fractures and heart disease, which are conditions that HRT combats.
In the UK two million women were taking HRT at its 2001 peak, but the number has now plunged to one million.
Dr Stevenson added: 'For most women suffering from menopausal symptoms I would advise them to have HRT without question.