Scientists found that women taking oral HRT were between two and three times more likely to develop a clot than those not using the treatment to control menopausal symptoms.
But there was no significant increase in the risk for women using HRT patches, according to the study in the British Medical Journal (BMJ).
In the UK, HRT tablets are the most common form of the treatment used by women.
The research comes after experts said earlier this week the risks of HRT had been exaggerated, meaning many women had abandoned a treatment which could vastly improve their quality of life.
In the latest study, researchers, including Professor Gordon Lowe from Glasgow University, analysed 17 studies looking at HRT use.
Previous research has suggested a link between HRT use and venous thromboembolism (VTE) – a clot in the vein which can be fatal.
But the BMJ study is the first to assess how much the risk is increased, and variations between different forms of HRT.
They found that overall those taking oral HRT more than doubled their risk of blood clots.
The risks were highest for women in the first year of treatment.
The researchers, including experts from France, also found that risks increased further for women who were overweight, or genetically predisposed to suffering blood clots.
They called for more research to investigate why HRT patches did not appear to greatly increase the risk of clots.
The experts suggested that the difference between HRT pills and patches could be the different way the hormone oestrogen is absorbed into the bloodstream.
In an editorial also in the BMJ, Helen Roberts, from the University of Auckland, called for more research to look at the effects of HRT patches compared to pills.
"In the meantime," he wrote, "we can advise healthy menopausal women, aged 50 to 59, that the risk of VTE with oral preparations is 11 additional cases per 10,000 women per year for combined therapy, and two additional cases per 10,000 women per year for oestrogen only."
A conference in Madrid this week heard from members of the International Menopause Society (IMS), who said the risks from HRT had been overhyped.
Dr David Sturdee, the president of the IMS, said the BMJ report confirmed present knowledge about links between blood clots and HRT.
"However, although this is raised in hormone users when compared to non-users, the absolute risk is indeed very small as blood clots do not often occur in this age group in healthy women on no treatment," he said.
Professor Valerie Beral, professor of epidemiology at the University of Oxford, said
: "It's possible that the use of HRT patches carries less of a risk than oral HRT, but as the authors themselves say, this needs to be confirmed with more research."
ABOUT eight out of ten women will have menopausal symptoms. While HRT is seen as the main treatment to tackle these symptoms, other approaches can also help:
Some women find relief in alternative therapies, such as herbal medicines, including black cohosh and red clover.
Women should take regular exercise to tackle hot flushes and night sweats.
Reducing stress can also make symptoms less severe.
Changes to diet, such as avoiding spicy food, caffeine, smoking and alcohol can help to stop hot flushes.
To combat disturbed sleep, women should avoid exercise late in the day.
Relaxation exercises, such as yoga, can help mood problems.