Mr Thomson was one of the board members sacked by Dr Jonathan Coleman a month ago. He was then elevated to the commissioner's team to help sort out its affairs.
Last week, papers were released that showed officials told Dr Coleman changes to southern health services would be controversial, and would happen in a ''short period of time''.
It appeared to contradict official assurances that no big shake up was imminent. Officials said the risk to commissioner Kathy Grant's reputation justified a boost in her daily pay from $1062 to $1400.
When contacted on Friday, Mr Thomson said he had had no discussion about reputation risk, and as far as he knew, his contract did not include that provision.
''[Dr Coleman] was definitely not looking for slash and burn solutions. I'm my own man, and I'll make my own decisions based on good information and good evidence,'' he said.
He did not know why there was a discrepancy between what the official papers revealed, and the messages going to the public.
''All I can do is repeat what I've said ad nauseum, what the minister told me.
''There's no other way I can answer the question. Asking me it 30 different ways won't change it.''
The commissioner team had been open about the need for change in how services were delivered, he said.
''There will inevitably need to be change but we've been given no prescription for that change.
''[Dr Coleman's] looking for long term solutions and he doesn't believe this is a ship that can be turned around in a year, or even a couple of years.''
Labour's health spokeswoman Annette King said the situation was ''murky'' and she did not know what the Government expected or planned.
''It's always surprising when you read what's been going on behind the scenes and what's been said publicly - sometimes they don't match,'' she said.
It appeared the board would continue to receive deficit support, and it was unclear when it was expected to break even. When contacted on Friday, Mrs King had spent two days in the South with Dunedin North MP Dr David Clark visiting rural hospitals.
The pair had learnt a lot about the strengths and strains in the rural hospital network, she said.
