The Care Quality Commission tried to “gag” the doctor who led the Healthcare Commission’s investigation into Mid Staffordshire Foundation Trust, the public inquiry into deaths at the trust has heard.

Heather Wood, who transferred to the CQC when it succeeded the commission in 2009, was placed under a “gagging order” restricting her from criticising the regulator when she left last August after the abolition of the investigations team.

Dr Wood told the inquiry she did not have “great confidence” in the CQC uncovering similar failures as its registration regime was focused on detecting underperformance through non-compliance with its own standards, rather than identifying potential problems by learning “national lessons” of the type linked to problems at Mid Staffs.

Former Healthcare Commission chief executive Anna Walker told the inquiry she was concerned registration alone would not be “sufficient”.

Dr Wood was also critical of the regulator’s regional structure, which she suggested allowed relationships between the regulator and the regulated to become too cosy, and claimed NHS West Midlands had exerted undue influence over the CQC.

She said the strategic health authority had contacted “very senior staff” at the CQC during an investigation into GP out-of-hours service Take Care Now, resulting in criticism of the SHA being toned down in the final report.

Dr Wood also blamed pressure exerted by NHS West Midlands on CQC chief executive Cynthia Bower for a U-turn on a decision to conduct a preliminary investigation at University Hospital of North Staffordshire Trust in 2009.

Dr Wood said she had felt the investigation team’s “cards were marked” from the early days of the CQC, meaning it would be disbanded.

In her submission to the inquiry, Ms Walker also said Monitor and NHS West Midlands were keen for the commission to speed up the investigation to limit bad publicity while NHS chief executive Sir David Nicholson and the NHS leadership team were not “comfortable” with the idea.

The inquiry also heard that former Healthcare Commission and CQC communications lead Roger Davidson was subject to a gagging order. He revealed former commission chair Sir Ian Kennedy had threatened to resign if then health secretary Alan Johnson did not retract criticisms he had made of the commission’s actions regarding Maidstone and Tunbridge Wells Trust. The comments were withdrawn.

The inquiry continues.