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Mr Roper is concerned that two patients are still being treated for depression with ketamine, which is not licensed for that purpose.
The National Health Board (NHB) announced last July it was investigating whether use of the drug in the Dunedin mental health service was experimental.
The NHB handed the matter to the Health and Disability Commissioner, where it still lies. The commissioner is yet to report back.
Southland chief medical officer David Tulloch told the Otago Daily Times in a statement this week that ketamine as a treatment for depression was stopped while the commissioner's investigation was under way.
However, two patients requested to resume the treatment after "positive clinical responses".
"This request went through a thorough process to ensure its clinical appropriateness and fully informed consent," Mr Tulloch said.
Clinicians can prescribe drugs off-label, but not for experimental use.
Chief executive Carole Heatly said in a statement that issues raised in Mr Roper's letter were strongly disputed, and the DHB was seeking legal advice.
"I have met with Mr Roper to discuss the letter and am satisfied with the DHB's conduct concerning his employment."
In the letter, Mr Roper said he took a stand in 2010 over ketamine, which eventually led to him choosing whether to "do my job and lose my job or don't do my job and keep my job".
He left the DHB on June 1, after more than six years as Otago mental health consumer adviser.
Not all of Mr Roper's claims can be reported, as they relate to a clinical case. However, he claims senior managers carried out "attempted cover-ups" .
"The substitution of this treatment for more accepted and to date better-evidenced treatments is unconscionable," he wrote.
"[For] almost 18 months the SDHB has acted as though it is actively [seeking] to suppress discussion, [and] refused to debate or acknowledge the issue of informed consent of people who are clearly unable to give the degree of consent required."
Mr Roper felt "targeted and victimised" by an investigation into his personal business interests, which he felt was linked to his being a whistle-blower.
Ketamine is licensed by Medsafe as a fast-acting general anaesthetic, and is used for pain relief in milder doses. It is a class C-controlled drug, used recreationally for its hallucinogenic effects.