Northern Territory Police Commissioner John McRoberts has resigned amid a formal investigation into his conduct.

Acting Chief Minister Peter Chandler accepted the resignation, citing a perceived conflict of interest.

The resignation followed allegations the commissioner involved himself in a criminal investigation where his relationship with the subject of that investigation gave rise to a conflict of interest, Mr Chandler said in a statement.

The ABC understands the criminal investigation related to Darwin travel agent Xana Kamitsis.

Ms Kamitsis was arrested last November as part of an investigation into the alleged rorting of a government travel subsidy scheme.

The case is currently before the courts.

Mr Chandler said in a statement the Government had lost confidence in Mr McRoberts and his position had become untenable.

At a press conference on Wednesday afternoon, Mr Chandler refused to give more information about how Mr McRoberts had involved himself in a criminal investigation, or which investigation.

However, Mr Chandler said "the evidence would suggest" Mr McRoberts had involved himself in the investigation to the point "there may have been some influence".

He would not say whether Mr McRoberts's relationship with the subject of the investigation was personal or professional.

Mr Chandler said he became aware of the allegations on Friday night.

"Over the weekend that information has been thoroughly investigated," he said.

"We have had everyone from my staff through to the Solicitor-General ensure that we take that information and follow through.

"In this case here, after speaking to my Cabinet colleagues, including the Chief Minister, we saw that there was a loss of confidence in our police commissioner, leading to accepting his resignation today."

Mr Chandler said it was important that the Government and the public had confidence in their police commissioner.

"Their integrity must be beyond reproach," he said.

"John McRoberts lost my confidence and I acted swiftly as soon as I became aware of the matter."

Mr McRoberts joined the Northern Territory Police in 2009 after a 31-year career with West Australian police.

Assistant Commissioner Reece Kershaw has been appointed Police Commissioner.

The former assistant commissioner of crime and specialist services, Mark Payne, has been appointed Acting Deputy Commissioner.