The head of England's NHS regulator, Cynthia Bower, has resigned after growing criticism that the watchdog was not fit for purpose.

Bower, chief executive of the Care Quality Commission (CQC), announced that she is quitting her £195,000-a-year post after four increasingly difficult and controversial years at the helm.

Concern over the watchdog grew in the Department of Health last year after organisations including care home operators and the NHS Confederation, which represents hospitals, voiced their fears that their establishments were not being policed properly by the CQC.

A Whitehall sources said: "Ministers had been assured that the CQC's house was in order. But each time they opened a door, skeletons fell out."

Paul Burstow, the social care minister, is said to have become uneasy after repeatedly hearing complaints from care home providers, residents and relatives that the CQC was not enforcing basic inspection standards.

Unions representing NHS staff and patient charities such as Action on Elder Abuse and Action against Medical Accidents also voiced grave reservations about the body's effectiveness.

Andrew Lansley, the health secretary, and his ministers were so worried by the CQC's apparent failings that they brought forward its performance and capability review, planned for later in this parliament, to investigate the concerns as a matter of urgency.

That report, published on Thursday, contained some praise but also confirmed key failings in the CQC's performance, such as some managers' inadequate training.

Bower's departure was portrayed as a personal, voluntary decision because she felt it was "time to move on", and Whitehall sources said she "was not pushed".

But she is thought to have decided to quit before, as expected, she personally and the CQC in general are criticised in three forthcoming reports.

"This is Cynthia Bower's calculation of the best time to get out, given what's coming down the track," said one official. "She decided to walk. She's gone before pressure would have forced her out."

The assessment of the CQC by the Commons public accounts committee (PAC) will be "damning", with MPs on the panel discussing whether to call for Bower's resignation in it, sources said.

The Department of Health also plans to review how the CQC handled the scandal of Winterbourne View, a private hospital near Bristol for people with learning disabilities. The CQC admitted that it ignored a whistleblower, former charge nurse Terry Bryan. He then went to the BBC, whose Panorama programme revealed sickening abuse of patients, leading to an outcry, 10 arrests and the home's closure last June.

But the most serious criticism of Bower is likely to come from the year-long public inquiry into how NHS bodies failed to prevent between 400 and 1,200 patient deaths due to poor care at Stafford hospital.

In 2009 Lansley, then shadow health secretary, questioned Bower's suitability to lead the newly-created CQC because critics claimed she had done too little to investigate relatives' claims of appalling treatment when she ran the NHS's West Midlands strategic health authority.

The inquiry heard severe criticism of how she responded to the emerging evidence about Stafford hospital's care, especially in its A&E unit.

Although the CQC said Bower will be staying on until the autumn, there is a belief in Whitehall that either the PAC report, due in the next few weeks, or the Stafford report, expected in April or May, could make that untenable.

The CQC said: "Cynthia Bower will continue to collect a salary until she leaves the CQC, commensurate with the fact that she continues to perform a full time role up to that point, but there will be no final 'lump sum' payment."

Ministers welcomed Bower's decision as a chance to refocus a body that has been beset by infighting, poor morale and claims of bullying, and has been severely criticised by the health select committee and National Audit Office. The committee highlighted the CQC's "significant distortion of priorities" for putting registration of care providers above inspections. The NAO castigated it for "significant failures that put patient care at risk".

Bower has admitted that the CQC's initial "light-touch" regime did not work or command confidence. It switched to a much more robust approach last year, including unannounced inspections, after Lansley made clear his concerns.

In a brief statement, Lansley said: "I would like to thank Cynthia for her work and leadership and wish her the best of luck for the future. Over the last year, we have seen CQC make improvements and respond to the need for enhanced scrutiny and enforcement of standards."

David Stout, the NHS Confederation deputy chief executive, said the performance and capability review of the CQC showed that the government "has listened carefully to the points we have been putting forward".

"An effective regulator needs to work with and earn the confidence of the organisations it regulates. We have made the point that the inspectors are not always earning the confidence of the organisations they visit because their knowledge is too generic."

Pressure for a shakeup of the CQC intensified last November after two internal whistleblowers gave extraordinary evidence about its failings in the Stafford hospital inquiry.

Kay Sheldon, a CQC board member, and Amanda Pollard, a CQC inspector from Kent, claimed that patients' lives could be at risk because the regulator was performing so badly it might not spot another scandal.

They claimed some staff were not properly trained for their jobs, the CQC had a culture of bullying, was beset by low morale and lacked a clear view of what it should be doing. Sheldon said Bower and the chair of CQC, Dame Jo Williams, had put "reputation management and personal survival" above patients' interests.

Sheldon said Bower's departure was necessary and overdue. "This is the right decision for CQC and for the future of regulation," she told the Guardian.

"People will not be surprised to learn that I believe Cynthia Bower should have left before now given the serious and ongoing problems the organisation has faced.

"It is an inescapable fact that the board has not provided the necessary leadership and scrutiny. The persistent failure to address, and at times acknowledge, the problems needs to be tackled if we are to achieve an effective and sustainable regulator that functions in the interest of patients and the public."

Williams should leave too, in order to restore the CQC's credibility, added Sheldon.