The Royal Wolverhampton Trust took the unusual step of naming the medical professional, who raised concerns of unconventional cancer treatment.
It issued a press release stating he was under investigation for 'serious misconduct' about an unrelated matter on its website in response to media inquiries about the chemotherapy affair.
The Express & Star has chosen to respect the person's anonymity. A separate statement by hospital clinicians claimed the whistleblower was facing legal action from two patients for poor practice.
Dr David Drew, who had highlighted failures at Walsall Manor Hospital, said: "The treatment of this person is atrocious. There is absolutely no protection for people who raise these sorts of concerns. It is disgraceful the trust would also attempt to discredit him by bringing up unrelated cases.
"I think this demonstrates there is no political will whatsoever to protect whistleblowers despite the Francis Inquiry into the Stafford hospital scandal."
In that report, Sir Robert Francis QC urged the NHS to protect whistleblowers and encourage staff to speak out about their concerns.
It said there were lots of examples of organisations supporting whistleblowers. But it also said too many were put off speaking up because they 'fear victimisation', while others do not raise concerns because they feel they will not be listened to.
The review heard stories of staff that have faced isolation, bullying and counter-allegations.
In some extreme cases when staff had been brave enough to speak up their lives had been ruined, it said. NHS trusts will have to appoint a guardian to help whistleblowers in England.
New Cross said it does protect whistleblowers and take concerns raised by staff seriously.
Express & Star editor Keith Harrison said: "Legitimate whistleblowers who seek anonymity should be protected and their claims investigated thoroughly.
"Lessons must clearly be learned from the Francis Inquiry if we are to have the transparency and scrutiny the NHS both deserves and needs."