Australian Greens federal Senate hopeful Simon Sheikh has conceded he's missed securing one of the two ACT seats in the upper house.

The Australian Electoral Commission (AEC) is due to confirm the outcome on Tuesday.

Mr Sheikh congratulated his opponents, Labor senator Kate Lundy and Liberal Zed Seselja who was running for the Senate for the first time.

While Senator Lundy had secured the votes to ensure her place, Mr Seselja is relying on preferences for his likely success.

With nearly 95 per cent of votes counted, Mr Sheikh secured 19.25 per cent (47,288) of the primary vote.

But preferences had worked against him.

"The Animals Justice Party's decision to preference the Liberal Party ahead of the Greens has made it incredibly difficult for the Greens to win this Senate seat," he said in a statement on Thursday.