The comments by Matthew Bonson, the member for the Darwin electorate of Millner, were detailed in a memo sent to the Labor Party's four other Aboriginal M-Ps in the territory.
He says the Martin Government risked an electoral backlash, following the recent debate over violence in indigenous communities.
In the document, Mr Bonson said he was concerned by the feedback he had received from the local community, which included a high level of misunderstanding and even hatred towards the Chief Minister.
He also suggested the Indigenous Affairs portfolio should be given to one of the two Aboriginal ministers in cabinet.
But, in a statement released by the Northern Territory government, Mr Bonson described his comments as ill-informed and wrong.