Despite speculation a vote of no-confidence in Mr Mills would be called, CLP director Tory Mencshelyi said a vote of confidence was instead held.
Ms Mencshelyi said delegates voted unanimously in favour of the motion.
Mr Mills has angered some in his party over a decision of his government to hike up electricity prices by 30 per cent and initiating a cost-cutting program since taking office late last year.
He has cited debt left over by the former Labor government as reasons for the spending cuts and revenue raising measures.
Last week NT Attorney-General John Elferink began counting numbers ahead of what was an aborted leadership challenge.
The move highlighted the divisions within the parliamentary party, which seized power in the NT last August in a landslide.
Mr Elferink offered his resignation but was ultimately allowed to keep his portfolio.