Adam Giles has become the first Chief Minister in the Northern Territory to lose his seat while in government, after final postal votes counted showed a Labor victory in the Alice Springs seat of Braitling.

Labor have never won an urban Alice Springs seat since self-government, but Labor's Dale Wakefield secured victory with a 20 per cent swing.

"Last few weeks have been very, very humbling," Ms Wakefield said.

"A lot of people changed their vote … I take that responsibility very seriously."

Mr Giles has put blame on the ABC Four Corners episode that showed years of abuse inside NT youth detention centres.

"When the Don Dale case came up I thought I would be a losing seat," Mr Giles told AAP.

"I won't challenge it, I didn't expect a different result."

The Territory's Labor landslide election, which saw the Country Liberals crippled to just two seats, and Labor to win 18, has also seen CLP president Tory Mencshelyi resign.

"I always said when I took on the position that I would take it on for a year," Ms Mencshelyi said.

But the newly formed Labor Government has suffered its own surprise defeat, with Deputy Leader Lynne Walker losing to newcomer independent Yingiya Mark Guyula.

"I'm excited," Mr Guyula said.

"I feel good, comfortable and just staying calm."

The victory will leave Labor without one of its most experienced and respected parliamentarians.

Labor insiders were wary of Ms Walker's defeat after Mr Guyula, who had campaigned on establishing a treaty between the Yolgnu people and the NT Government, polled strongly in Arnhem Land booths during the federal election.

"Indigenous people … have felt left out and we have felt that we've been starved out of funding," Mr Guyula said.

Count could be challenged

But Labor president Syd Stirling has pointed that the party could challenge the count.

"Our scrutineers are reporting more than enough inconsistencies and irregularities within the ballot process," Mr Stirling said.

"We've been considering our position over the next few days."

The final deadline for postal votes was noon on Friday, with the final count showing Labor at 18 seats, five independents and the CLP at just two.

The official results will be declared on Monday.

ABC/AAP