The medical director of the NHS, Professor Sir Bruce Keogh, has said that hospitals should either cremate or bury the bodies of foetuses which have been aborted, rather than destroying them in hospital incinerators.
The call comes after Channel 4's Dispatches programme revealed earlier this week that ten NHS trusts have been burning the bodies of aborted foetuses in incinerators used for the disposal of rubbish and clinical waste.
The undercover documentary producers also claimed that two other hospital trusts had been burning deceased foetuses in incinerators used for the heating of hospitals.
They even discovered that some women had not been consulted before the bodies of the foetuses they had carried were incinerated.
Health minister Dr Dan Poulter was quoted by the BBC describing this practice was "totally unacceptable".
"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," said Dr Poulter.
He also said that Sir Brice has "written to the Human Tissue Authority to ask them to make sure that there is clear guidance on this issue".
HTA guidelines say that women who have an abortion should be made aware of three options regarding the foetus's body - burial, cremation and incineration.
The guidelines are quoted by the BBC as saying that handling an aborted foetus is a "sensitive" issue, and that if incineration is used, the foetus should not be destroyed alongside other forms of clinical waste.
In portions of his letter on the matter quoted by the BBC, Sir Bruce goes a step further and argues for incineration of foetuses to be stopped altogether.
"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 foetal remains is inappropriate practice and that other methods offer more dignity in these sensitive situations."
Professor Sir Mike Richards, the Care Quality Commission's chief inspector of hospitals, was quoted by the BBC saying: "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."
Sir Mike pointed out that the CQCs powers were extensive, and that they could "inspect unannounced" if they felt it was warranted.
Paul Tully, the General Secretary of Society for the Protection of Unborn Children, welcomed the Dispatches investigation, and the moves of Sir Bruce and Sir Mike on this matter. But by his reckoning, neither had gone far enough.
"We insist that the answer is not as simple as having a new code of practice or better ways of treating babies' remains," he said.
"We must stop killing babies like these by abortion and then we will know how to respect the dead.
"Until we reject the abortion culture and learn to honour all mothers – including expectant mothers and bereaved mothers - the sickening consequences of aborting over 500 babies every day will continue to resurface and unsettle us."
In 2011, there were 189,931 abortions carried out in England and Wales, mostly by the NHS.