A senior Department of Health manager is under investigation by the General Medical Council over allegations that she ordered a hospital trust to hit its waiting list targets “whatever the demand.”

Dame Barbara Hakin, director of commissioning at the Department of Health and a GP, is alleged to have issued the order to the United Lincolnshire Hospitals NHS Trust, putting patient safety at risk, in her former role as chief executive of the East Midlands Strategic Health Authority.

The complaint was made to the GMC last year by the Private Eye columnist Dr Phil Hammond, who was responsible for exposing the Bristol children’s heart surgery scandal in the 1990s.

Today Dr Hammond said the complaint was “active and ongoing, and at a senior level.” He added: “But the GMC moves at the speed of a glacier.”

Gary Walker, former chief executive of the United Lincolnshire Hospitals NHS Trust, who was sacked in 2010, today breached the terms of a gagging clause in his £500,000 severance agreement to speak out about the pressure he was put under for the first time.

He accused NHS chief executive Sir David Nicholson and senior NHS leaders of putting targets ahead of patient safety and said he warned them of the dangers after he joined the United Lincolnshire Trust in 2006.

“By April 2009 demand [at the trust] was out of control and fearing patients were coming to harm, I explained to Barbara Hakin that I was going to get an external review into mortality. I was told to resign or my 20-year NHS career would be in tatters,” he said in a statement.

The trust was last week named as one of 14 with high mortality rates being investigated in the wake of the Francis report which exposed appalling care between 2005 and 2009 at the scandal-hit Mid-Staffordshire NHS Trust.

The SHA said yesterday it “totally refuted” Mr Walker’s claims and had always acted “in the interests of patients”. The Department of Health said Mr Walker’s allegations had been independently investigated and “found to be without merit.” The GMC said it could not comment on an individual case.