Deposed Northern Territory chief minister Terry Mills is returning home from Japan but says he stepped aside after learning he had been defeated by Adam Giles.

Mr Mills discovered his fate during a break in a business meeting in Japan when phoned by acting chief minister Willem Westra van Holthe.

Mr Giles, who was the NT's transport minister, becomes Australia's first indigenous head of government after his second challenge to Mr Mills' leadership in less than a week.

Mr Mills has cut short his meetings and will fly home as soon as he can but says he accepted the decision imparted by Mr Westra van Holthe.

"He advised me that this is real, that it appears that there are numbers insufficient for me to continue," Mr Mills told ABC radio in Darwin on Wednesday.

"As I have always sought to do the right thing and act in the best interest of the Northern Territory, and albeit (it was) not possible to continue in these circumstances as chief minister, not having sufficient support ... I then stepped aside from that position."

Mr Mills said he would not be leaving the CLP as "that's not my style", and would support Mr Giles.

"He will have my support because I am here to serve the best interests of the territory."

Asked if he felt betrayed, Mr Mills said he thought his colleagues had been under a fair bit of pressure to find a "way forward".

He said he would go back and talk to them.

"But my main business is to make sure we get on with the job of serving the territory well."

Asked if he thought Mr Giles would make a good leader, he replied "probably".