Whistleblowers will be deterred from coming forward after an NHS inspector who highlighted key failures lost her employment tribunal, campaigners have warned.

Amanda Pollard told a public inquiry into the Mid Staffordshire scandal in 2011 that the Care Quality Commission, where she worked, prioritised paperwork over looking for poor standards of care. Her criticisms were largely accepted by the inquiry and the regulator’s new leaders, but she left the CQC last year, claiming she was forced out.

An employment tribunal has rejected Mrs Pollard’s claim for unfair dismissal, even though it acknowledged that she was making public interest disclosures and it was “wholly inappropriate” for bosses to criticise her for doing so. The tribunal ruled that while she suffered because of her revelations there was no campaign against her.

A judge said that it was wrong for Dame Jo Williams, who was CQC chairwoman at the time, and Cynthia Bower, then its chief executive, to send emails to all staff criticising her. “There was no acknowledgement or recognition that [Mrs Pollard] might be expressing genuine concerns in the best interests of the public whom [the CQC] sought to service,” Harjit Grewal, the tribunal chairwoman, wrote.

This was “particularly surprising” given that the CQC relied on NHS whistleblowers to raise concerns about poor care. However, Grewal said that Mrs Pollard had misinterpreted “innocuous” actions by other managers.

Mrs Pollard said the decision “sends a very unfortunate message. It’s got be a quietening message for whistleblowers and that’s very unfortunate. When care is bad, people do need to pipe up about it and the law needs to protect them.

“There is still a real fear factor about whistleblowing, which prevents people from speaking up – especially if this is in order to support those facing litigation. Despite many messages of support from former colleagues, I found it difficult to call them as witnesses.”

Cathy James, chief executive of the charity Public Concern at Work, said: “This case clearly demonstrates how difficult it is to prevail as a whistleblower through the UK courts. The public interest is often lost in the legal wrangling surrounding these types of cases. Whistleblowers need more support and are often facing a David and Goliath battle.”

David Behan, chief executive of the CQC, said: “In the lead-up to the tribunal we offered Ms Pollard a new job. We have made a number of changes to encourage an open and transparent culture and improved the way we engage with staff.”

Mrs Pollard is not alone. Sharmila Chowdhury was a radiology manager for Ealing Hospitals NHS Trust who lost her job after telling it that £250,000 had been lost through moonlighting by medical consultants. Ms Chowhury took the trust to a tribunal and won, but it refused to reinstate her.

Simon Stevens, chief executive of NHS England, has agreed to meet six whistleblowers later this month. The six, who want independent reviews into their cases and a public inquiry led by a judge, have won cross-party backing and support from several senior NHS experts.

Mr Stevens and Jeremy Hunt, the health secretary, have discussed reforms with a number of those who have exposed some of the worst NHS failures, including Julie Bailey, who brought the Mid Staffordshire scandal to public notice.