Shyam Kumar worked part-time for the CQC as a special adviser on hospital inspections, but Manchester Employment Tribunal found he was unfairly dismissed.
Between 2015 and his dismissal in 2019 he had reported concerns regarding inadequate hospital inspections, staff bullying and serious patient harm.
The CQC "accepted the findings".
Mr Kumar’s concerns included a group of whistleblowing doctors being prevented from discussing their concerns at a hospital inspection.
He also reported concerns about a surgeon at his own trust, Morecambe Bay, who had carried out operations that were "inappropriate" and of an "unacceptable" quality and harmed patients.
He warned the CQC that the trust management wanted to bury it "under the carpet". The tribunal noted his concerns were found to be justified and the surgeon eventually had conditions placed on his licence to practise.
The tribunal's judgement confirmed the safety issues Mr Kumar raised played a significant role in his dismissal.
"It is very clear that the emails and concerns raised by Mr Kumar had a material impact on the decision to disengage him," it said.
The CQC said: "We accept the tribunal findings and have learnt from this case.
“We have already improved many of our processes and will continue to review these based on the findings to ensure we make any further necessary changes."
Mr Kumar was supported in pursuing his legal challenge by the British Medical Association (BMA).
Welcoming the tribunal’s judgement, BMA council chair Philip Banfield said: “It is absolutely paramount that doctors are able to raise safety concerns without fear of recrimination or backlash from employers.
“This judgment clearly underlines the fundamental need to protect whistleblowers and is a significant legal victory that the BMA is proud to have supported.
“That such a case happened within the very organisation that is meant to safeguard standards within the NHS and social care is incredibly concerning indeed and the CQC must answer serious questions about its culture and the policies that allowed this to happen.
“The BMA is clear that the NHS and the whole health and care system must have an open, learning culture where doctors and their colleagues can be confident in speaking out when they see patient safety at risk, and we are committed to safeguarding our members’ whistleblowing rights wherever they work.
Rather than punishing those who bravely speak up, the system should be supporting them, so that steps can be taken to improve safety for both staff and patients.
Mr Kumar has been awarded £23,000 in compensation resulting from injury to his reputation.
