An NHS Trust is using a gagging order in a "cover-up" to prevent patients from discovering that they were operated on by an "untrained" cancer surgeon against national guidelines.

An MP has called for a parliamentary inquiry after revealing in the House of Commons that at least 100 patients were operated on by the gynaecologist at a Swansea hospital over a three-year period.

The Trust refused to alert the women "that they had been operated on by an untrained surgeon", the Liberal Democrat MP John Hemming told the Commons, despite several senior colleagues raising concerns about the surgeon's competency to perform the operations, he said.

Instead, since 2008, Abertawe Bro Morgannwg University Health Board has spent more than £375,000 of taxpayers' money – the equivalent of employing 20 nurses – obtaining an injunction to prevent a junior doctor from informing the patients about his concerns. The junior doctor was sacked in 2008.

The Trust insists that the gag – which includes the media and MPs – was obtained to protect patient confidentiality from the original whistleblower, who kept threatening to contact them. It is not known whether or not any of the patients have since suffered harm or complications.

Mr Hemming told MPs that the whistleblower had reported his concerns to South Wales Police and the regulator. Mr Hemming, who campaigns on the misuse of injunctions against the public interest, said that the Trust's actions amounted to a "cover-up".

He said: "Dr Paul Flynn, a consultant obstetrician and gynaecologist... from 2002 to 2005 performed over 100 operations on cancer patients against national guidelines. Concerns about Dr Flynn had been passed since 2003 to medical director, Dr John Calvert, who had hired him.

"However, Dr Flynn was only prevented from treating cancer patients in May 2005 after six surgeons complained directly about his poor respect of tissues, questionable knowledge of anatomy, lack of appreciation of what is on X-rays, and lack of a realistic surgical approach to cancer."

The MP, who has previously used parliamentary privilege to break a super-injunction taken out by footballer Ryan Giggs, told The Independent: "What particularly worried me is that the Welsh Health Minister indicated that the injunction prevented her from investigating. It is clear that a parliamentary inquiry is needed to get to the bottom of this issue and review the misuse of legal proceedings."

The Trust last night said it "completely refutes" the allegations made by Mr Hemming and had "full confidence in the ability" of Dr Flynn, who works as an obstetrician and gynaecologist with a special interest in oncology and diseases of the vulva.

"These accusations have been thoroughly investigated by police, the General Medical Council and others organisations and found to be totally baseless... it is unfortunate that [Mr Hemming] chose to make the comments, under parliamentary privilege, thereby potentially causing alarm to patients."