The move is designed to gather more information on the practice, which was outlawed in the UK in 1985.
The children's charity, NSPCC, which set up a FGM helpline seven months ago, says it has already received 153 calls.
At least 66,000 girls and women in the UK are believed to be victims of FGM.
On Thursday, the United Nations is marking a Day of Zero Tolerance to FGM.
The Department of Health says from April, all NHS hospitals will be able to record if a patient has undergone FGM or if there is a family history of this.
By September, all acute hospitals will have to report this data to the Department of Health, on a monthly basis.
Continue reading the main story Somalia - more than 97% of women aged 15-39 have been cut in this way Guinea - 99% of women aged 35-39 and 89% of those aged 15-19Egypt - 96% of women aged 35-39 and 81% of those aged 15-19Sierra Leone - 96% of those aged 35-39 and 75% of those aged 15-19Source: International Development Committee, June 2013
The government says this is the first stage of a wider scheme to improve the way the NHS will "respond to, follow up and support the prevention of FGM".It is hoped this will, in the autumn, provide the first snapshot of how many women have been treated by the NHS for FGM, and in the longer term, help identify families where girls might be at risk.
So far, no-one in the UK has been prosecuted for carrying out FGM.
The NSPCC said of the 153 calls it had received to its helpline, 40% had been referred to local authorities and in the remaining 60% of cases it had offered specialist FGM advice.
The charity said it had set up its service after discovering that more than 1,700 victims of FGM had been referred to specialist clinics in the past two years.
It said 41% of calls received had come from worried professionals, particularly midwives, doctors and teachers, while some 22% were from worried parents, carers and other relatives.
'Big problem'FGM is most common among some African, Asian and Middle Eastern communities.
But campaigners say there is a lack of knowledge about how prevalent the practice is and where it is happening and that this is hampering social services and the police in the collection of evidence.
Comfort Momoh, who runs the African Women's Health Centre at Guy's Hospital in London, says FGM is "a big problem in the UK" and that health workers need to be better informed about it.
"We have people migrating from different parts of the world coming to the UK, to the West, bringing their cultures, bringing their own traditions, so it is a big problem - and it is growing - so as a front-line provider we need to educate ourselves.
"We need to be aware of what to do and how to safeguard children and girls."
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