THE ALP in the Northern Territory received a political bloody nose on Saturday, courtesy of a backlash from indigenous voters.

Labor will now try and come to grips with huge swings against it in seats that have been safe territory for years and work out a strategy to win them back.

A swing of more than 50 per cent against an ALP candidate who stood unopposed four years earlier, a 15 per cent swing in Katherine and a 16 per cent swing in the electorate of Stuart are just some of the more startling results.

Seven years ago, Labor held 19 seats in the 25-seat NT Legislative Assembly.

For the next four years it may hold as few as eight seats, although counting continues and could deliver it one or two more.

At least two people who served as ministers in the Henderson government - Malarndirri McCarthy and Rob Knight - have lost their seats.

There is little doubt the size of the change indicates more than minor pockets of discontent with Labor.

It shows Labor that traditional supporters - indigenous Australians - are fed up with their policies, and see the Country Liberal Party (CLP) as a viable alternative.

Undoubtedly local factors, such as the creation of eight "super shires" by amalgamating 63 small councils, played a part, with some in the bush fearing they were losing their voice.

But federal Labor should be watching the results closely.

The intervention in Aboriginal communities, started by John Howard and re-named Stronger Futures after the ALP took it over, has been deeply unpopular in many indigenous communities.

Some Aboriginal leaders have said the laws unfairly branded particular communities as harbouring drunks and paedophiles and unable to manage their own affairs.

"Traditional people have not been given proper respect," NT's chief minister-elect Terry Mills told journalists on Sunday.

media_camera Terry Mills celebrating after the success of the Country Liberal Party. Picture: Michael Franchi

He said the federal government's decision to ban the live cattle trade with Indonesia - which went down badly among pastoralists - also played a part in the vote.

"I think that was ideologically driven and politically driven," he said.

Labor held its urban seats, in what some have said was evidence it focused too narrowly on the electorates that traditionally decide who wins the NT poll, at the expense of rural areas.

In a break with tradition, Labor leader Paul Henderson did not appear before the media on Sunday.

After such a deep loss there will almost certainly be questions over his authority to continue as leader and people in the Northern Territory will be asking why he was ducking for cover.

Peter Rudge, who was convicted of manslaughter in 1998 for shooting Michael Anthony Lewis seven times, only secured 149 votes with 73 per cent of the vote counted.

Mr Rudge had campaigned on trying to get better rehabilitation programs for prisoners.

In the seat of Nightcliff where he was standing the Labor Party's Natasha Fyles looks likely to win the seat, despite a swing towards the Country Liberal Party of just over one per cent.

Earlier, Prime Minister Julia Gillard congratulated Mills after the Country Liberal Party's decisive win in Saturday's election.

"Prime Minister Julia Gillard today congratulated Terry Mills and the Country Liberal Party on their win in the Northern Territory election," a statement from the Prime Minister's office said.

A spokesman for Ms Gillard confirmed this morning that the Prime Minister had called Mr Mills to personally congratulate him.

The majority of the nine-paragraph press release was devoted to praising the legacy of outgoing chief minister Paul Henderson, with only two references in it to Mr Mills.

Ms Gillard said in the statement Mr Henderson had been dynamic and courageous during a time of expansion and change.

media_camera Outgoing Chief Minister Paul Henderson managed a smile. Picture: Katrina Bridgeford

"He leaves the position of chief minister with an outstanding record of achievements in health and education, including a huge boost for education for remote indigenous communities," she said.

"Importantly, he leaves an economy in superb condition, with an unemployment rate of just 4 per cent, down from 7.4 per cent, the envy of the developed world."

Trade Minister Craig Emerson says the NT election was fought on local issues rather than a reflection of Labor's fortunes federally.

"I've always maintained people are more than intelligent enough to separate federal from state issues," Mr Emerson told ABC TV today.

"I think the truth is ... outside of Darwin super councils were a real issue."

Dr Emerson said he wouldn't go through the entrails of the result but praised the work of Mr Henderson who had done a fantastic job lowering the unemployment rate and investing in education and health.

Last night, the Country Liberal Party seized power in the Northern Territory, bringing to an end 11 years of Labor rule.

"Tonight Territorians have spoken and I respect their decision,'' outgoing Chief Minister Paul Henderson said as he conceded the Australian Labor Party (ALP) had lost the election.

"My best wishes to Terry Mills, as he and the CLP will form the next government,'' Mr Henderson said at an ALP function in Darwin.

"He inherits a territory that is heading in the right direction,'' he said.

Rural electorates played a major part in the result, with big swings against Labor in remote areas and the ALP also losing the Darwin seat of Daly.

For the CLP the victory is the first electoral success the conservative party has tasted in the NT since it won the 1997 election.

The party campaigned hard on the issue of law and order and bringing the territory's budget back into surplus.

Mr Henderson said he was proud of his government's achievements and the creation of thousands of jobs.

Originally published as Indigenous tell NT ALP 'we matter'