Warning over burning aborted foetuses
The move by Prof Sir Bruce Keogh comes after it emerged that some hospitals have been burning foetuses as clinical waste.
Channel 4 Dispatches programme says 10 NHS trusts have been burning remains alongside rubbish.
It claims two more disposed of bodies in incinerators used to heat hospitals.
Health minister Dr Dan Poulter said this practice was "totally unacceptable".
"That is why I have asked Professor Sir Bruce Keogh, NHS medical director, to write to all NHS hospital trusts, to make it clear that it must stop now.
"The chief medical officer has also written to the Human Tissue Authority to ask them to make sure that there is clear guidance on this issue.
"While the vast majority of hospitals are acting in the appropriate way, that must be the case for all hospitals and the Human Tissue Authority has now been asked to ensure that it acts on this issue without delay."
'Disappointed'
The HTA has a code of practice for the disposal of human tissue, which includes foetal remains, that hospitals should follow.
It says women who have had an abortion or miscarriage should be informed that there are different options available - burial, cremation and incineration.
It says disposal via incineration should be handled as "sensitive" and therefore should not be done alongside the burning of waste.
In his letter, Prof Keogh says he believes it would be better not to use incineration at all.
"While it is acknowledged that incineration is not illegal across the UK, existing professional guidance makes clear that the practice is inappropriate.
"I share the view that incineration of fetal remains is inappropriate practice and that other methods offer more dignity in these sensitive situations."
The Dispatches programme claims some women were not told that their aborted foetus would be incinerated as waste.
Professor Sir Mike Richards, chief inspector of hospitals, from the Care Quality Commission, said: "I am disappointed trusts may not be informing or consulting women and their families. This breaches our standard on respecting and involving people who use services and I'm keen for Dispatches to share their evidence with us.
"We scrutinise information of concern and can inspect unannounced, if required."
Sands, the stillbirth and neonatal death charity, said the practice of incinerating pre-24 week foetuses is unacceptable and that whenever possible, cremation should be used instead.
A spokesperson said: "Research has shown that the stage the pregnancy has reached when the baby dies is not an accurate predictor of the length and depth of the grief the parents will experience.
"Foetus is not a term that parents use or that should be used with them. From the day the pregnancy is confirmed they are expecting a baby.
"The death of a baby at any stage of pregnancy is a major bereavement with life long consequences.
"The care that parents receive cannot lessen their pain, but poor and insensitive care can and does make matters worse both in the short and the long term."
In 2011, 189,931 abortions were carried out in England and Wales, mostly on the NHS.