Jeremy Hunt has stepped up pressure to end the use of legal gags on whistleblowers as he faced calls for an independent inquiry into his own department's involvement.
In a letter to the chairmen of every Trust, the Health Secretary warned against a culture in some quarters of "institutional self defence that prevents honest acknowledgement of failure".
In order to avoid a repeat of the Mid-Staffordshire scandal it was vital to "recognise and celebrate staff" who had the "courage and professional integrity" to speak out over safety concerns, he suggested.
He called on all bodies to ensure their actions met both the letter and the spirit of NHS whistleblower guidance.
On Friday Mr Hunt warned United Lincolnshire Hospitals Trust that it faced action if it had wrongly tried to silence a former chief executive from speaking out about patient safety concerns as part of a unfair dismissal case settlement.
Gary Walker was threatened with legal action related to his reported £500,000 payout after breaking his silence to allege he was forced out of his job in 2010 because he put patient safety ahead of Whitehall targets.
The trust is one of 14 being investigated by health chiefs over high mortality rates in the wake of the public inquiry report into serious failures at Mid Staffordshire NHS Foundation Trust that led to hundreds of unnecessary deaths.
Mr Walker welcomed the Health Secretary's intervention as a "very positive move" but said the threat of action against him for an interview with the BBC's Today programme on Thursday had still not been lifted.
And he suggested that Whitehall had a hand in prompting the action and should also be investigated.
"The threat against me has still not been withdrawn, despite the reassurance that it should not be in place," he said in his latest interview with the programme.
"I don't think I want to be too negative about Mr Hunt. He has clearly taken a personal interest and said that he will personally carry out the investigation and get to the bottom of it."
He questioned though how the Trust had known in advance of his decision to speak out.
"The Trust were never contacted by me or the Today programme so somebody from the Department of Health, and I do not know who that was, clearly spoke to them.
"I don't think that Mr Hunt can investigate his own department so I think he should be looking for someone exceptionally independent from all of this so I don't think it should be a civil service investigation.
"The whole chain of command needs to be looked at if Mr Hunt wants to stand by the transparency agenda."
He has claimed that NHS chief executive Sir David Nicholson ignored him when he raised concerns about patient safety in 2009. He told the Daily Mail that Sir David was "not interested in patient safety" and called on him to resign.
The Francis Report into the Mid-Staffordshire scandal called for a ban on the use of gagging orders that prevented concerns being raised about patient safety.
Mr Walker was sacked in 2010 for gross professional misconduct over alleged swearing at a meeting but insists he was in fact forced out for refusing to meet Whitehall targets for non-emergency patients when the trust came under pressure because of soaring demand for beds for emergency patients.
He defended his acceptance of the so-called "supergag", which prevented him even from revealing the existence of the agreement, saying the saga had help break up his family, left him unable to pay his mortgage and left him with "no choice".
East Midlands Strategic Health Authority rejects Mr Walker's claims and insists that it acted at all times "in the interest of patients".