Chief Minister Natasha Fyles declared fifth-floor staffer Brent Potter the winner of the Fannie Bay by-election last night, despite a massive swing toward the Greens and CLP.

In an expected close contest, only 63 per cent of eligible voters turned up to vote, with CLP candidate Ben Hosking taking the initial primary vote 41.7 per cent (1394 votes) to Mr Potter’s 32.6 per cent (1089) as of 8pm last night.

But the Greens’ deal with Labor was expected to put Mr Potter over the line, with two-party preferred presences favouring him with 1745 votes compared to Mr Hosking’s 1597 by the time the NTEC stopped counting votes last night.

The bulk of the two-party preferred votes that put Mr Potter over the line came from the single voting booth of Parap.

Ms Fyles was jubilant.

“The constituents of Fannie Bay have been heard,” she said.

“They want a government that backs them and only a Labor Government can do that.”

Mr Potter, who is now the second fifth-floor staffer to win a by-election for Labor in the last year after Dheran Young, gave a reportedly short victory speech, thanking the shoppies union and former chief minister Michael Gunner.

“I want to say thank you very much for believing in me,” he said.

“I said I’d be a strong voice and I will be a strong voice over the next two years.”

Ms Fyles conceded that there would be “a lot of analysis of this result over the next days and weeks”.

A celebratory photo on ABC Darwin’s website showed Mr Gunner at the centre of celebrations, with his arm around Mr Potter to his right, and Deputy Chief Minister Nicole Manison to his left, with current Chief Minister Natasha Fyles to the far left.

Ms Fyles said the by-election result was disastrous for the CLP, having now lost two straight by-elections to a sitting government – making political history again in the NT for losing a seat to an incumbent government for now the second time.

CLP Leader Lia Finocchiaro tried to turn the loss into a positive, pointing to the primary vote result and suggesting it held positive indicators for the next general election.

“It’s a good night for the CLP and it’s a good night for Territorians who have clearly sent Labor a message,” she said.

“We’re also very encouraged by the fact that the CLP has had a six per cent swing towards it as an outcome of this election. That sets us up for a pathway to victory in 2024.”

Brent Potter said the lower than expected voter turn-out was indicative of general “happiness” in the electorate.

“I think at the end of the day people will come out to vote if they see fit to,” he told the NT News.

“I think, if anything, it is an indication they are actually happy.”

NT Electoral Commissioner Iain Loganathan said the voter turnout was “disappointing”.

“Turnout at the Daly by-election last year was 66 per cent which is a remote division,” he said.

“As an urban division a much higher turnout was expected.”

Counting of votes will continue on Monday. The official declaration will be held following the September 2 deadline for the return of postal votes.