Health Secretary Andrew Lansley is said to have been “shocked” by a letter from health regulator the Care Quality Commission (CQC) apparently expressing concerns over the costs of inspecting abortion clinics.
The chairwoman of the organisation reportedly said she had to divert resources and cut the number of inspections of hospitals and care homes as a result of the abortion investigation.
Health department sources said Mr Lansley was shocked by the letter, and that the CQC had not asked for more money, but could have had it if it had done so.
According to the Daily Telegraph, Dame Jo Williams wrote on March 23: "Such a request at short notice entails operation's management time in planning the visits, cancelling pre-planned inspections as well as the compliance inspector's time in carrying out the visits and drafting the reports.
"Add to this the anticipated enforcement activity that will inevitably arise and it is clear that this has a considerable impact on our capacity to deliver our annual targets."
She added that the abortion investigation meant that 580 other inspections were "foregone" and that the total cost would be about £1 million.
The Government announced last month that the investigation had shown that some doctors were breaking the law by "pre-signing" abortion consent forms.
Spot checks at more than 250 abortion clinics found evidence of blank forms being signed in anticipation of patients seeking a termination.
The law states that, except in emergencies, two doctors must agree for a woman to have an abortion.
Although doctors do not have to see the woman in person, they must certify that they are aware of her circumstances and why she wants to go ahead with the procedure.
Nurses, counsellors and other healthcare professionals can assess the woman before the forms are signed.
Of more than 250 clinics investigated, it was thought 15% to 20% might be breaking the law.
A Department of Health spokeswoman said: "The CQC's statutory duty is to uphold the law.
"The CQC was one of the organisations who warned us of this issue at the time, and agreed with us that a programme of inspections should take place as a proportionate response to the serious allegations being made.
"We would expect the CQC, like any good regulator, to be able to prioritise its inspections and are told that in this case they did so, so that no patients were placed at risk.
"The CQC has around 900 inspectors, only some of whom were involved in these inspections, the vast majority of which were completed within four days."
Shadow health secretary Andy Burnham accused Mr Lansley of "chasing headlines" by ordering the abortion investigation and questioned whether his request to the CQC was proportionate.
He told BBC Radio 4's Today programme: "In the middle of this inspection programme, the Secretary of State communicated the early findings to a newspaper, before the inspection programme was complete and before any statement had been made to Parliament.
"That gives the clear impression that Mr Lansley was chasing headlines rather than following due process and, indeed, compromised the independence of the regulator."
Tory former health secretary Stephen Dorrell said Mr Lansley's intervention had raised questions about the independence of the CQC.
Mr Dorrell, who chairs the Commons Health Select Committee, told Today: "What should have happened probably is that he should have drawn attention to the fact that this was an issue in the newspapers and invited them to consider that in the context of their other priorities.
"You always get into trouble in any walk of life if you claim for yourself the ability to determine one priority without looking at all the others."
He said: "We need to be clear whether the priorities of the regulator are genuinely determined independently by the CQC itself or whether the priorities are determined by the Secretary of State. Is it independent or is it not?"
He said it would be a "scandal" if a Treasury minister instructed the independent HM Revenue and Customs to examine the enforcement of tax law in the case of a particular taxpayer.
"It seems to me that's the principle we need to establish clearly which should govern the relationship between ministers and the CQC," he said.
Mike Farrar, chief executive of the NHS Confederation, told Today: "I think it is entirely legitimate that a Secretary of State faced with a particular issue ... might take a view that he would want the independent regulator to look into something as serious as this.
"But the point is, there was a work programme agreed for CQC that put priorities into other areas and I think it is entirely legitimate for the regulator to turn round and say 'Well, this might divert from other issues, is that what you would want to do?'."
He added: "I think we should be clear about the consequence of taking on additional work. Indeed, the Secretary of State could have provided additional money for that work to be undertaken."
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