The Northern Territory government says it has heard the message, after a big swing against it in the by-election for the seat of Wanguri.

Australian Labor Party (ALP) candidate Nicole Manison secured her place in the NT parliament after capturing 69.7 per cent of the two-party vote, late counting showed.

The result was about a six per cent swing towards the ALP from the last election, making the seat now the safest ALP electorate in the NT.

The ALP had called on voters to send a message to the Country Liberal Party (CLP) that rules the NT, and the government said it had heard it.

"This government acknowledges the message contained in the result tonight," NT Chief Minister Terry Mills said.

"We will continue to work with, and engage the community in this period of change."

Commentators had thought it would be tough for the CLP to win Wanguri, which Labor has held since 1989, particularly after recent 30 per cent electricity price hikes and government cutbacks.

The CLP had said the price rises were needed to alleviate the debt held by the public-owned Power and Water Corporation.

But Ms Manison said the result was Territorians sending Mr Mills a message he couldn't ignore.

"People are unhappy with his broken promises and unfair price hikes," she said.

The by-election was sparked by the resignation of former chief minister Paul Henderson.

Counting will continue on Sunday with about 89 per cent of the vote counted so far.