Liberal candidate Zed Seselja was fighting off a strong challenge from the Greens' Simon Sheikh.

Figures from the Australian Electoral Commission had Labor's Kate Lundy retaining her position, as expected.

However the situation with the second seat was unclear, with the Liberals and Greens neck and neck.

In the ACT 265,269 people are enrolled to vote.

With two Senate spots on offer, the quota for a win is 33.3 per cent of the votes.

However the large number of votes cast at pre-polling stations were not counted. The Senate votes were counted after the lower house seats were finalised.

With less than half the Senate vote counted, at 10.45pm the AEC had Labor on 33.88 per cent, the Liberals on 31.66 per cent and the Greens on 21.48 per cent.

The Greens said Mr Sheikh had attracted a strong ''below the line'' vote.

The Animal Justice Party, which has first place on the ACT Senate ballot paper - earning the so-called donkey vote - is directing its preferences to the Liberal Party ahead of the Greens.

However the Greens will benefit from preferences from most of the other minor parties.

Mr Sheikh said: ''All over the country we've seen a swing towards the Liberals.

''It's one of the largest in the history of the Liberal party.

''To see a swing against the Liberal Party here in Canberra is a testament to the more than 1000 people who've volunteered on the Greens campaign.

''Our numbers suggest this will come down to the wire.

''One thing we know for sure is that the long spoken belief that this seat is unwinnable has been smashed tonight.''

Earlier Senator Lundy said: ''It's a solid result for ACT Labor.

''Clearly there is a national swing against Labor but we've pretty well resisted that here in the ACT.

''I think the swing away from Labor nationally has been impacted by the fear of job losses here under the Liberals.''

Mr Seselja was not available for comment.

While the territory is allocated two places in the upper house, the states have 12 senators each, regardless of population.

The term of the territory's senators go for three years, ending at the general election, whereas the state-based senators usually serve fixed six-year terms, unless the Senate is dissolved earlier in a double dissolution.

At the 2010 election, Labor's ACT Senate team led by Senator Lundy scored about 93,000 votes, with 76,000 for the Liberals, led by then senator Gary Humphries, and 52,000 for the Greens, led by Lin Hatfield Dodds.

This year Mr Seselja won a preselection ballot to become the Liberal's Senate candidate, ending Mr Humphries' decade-long career in the Senate.

Mr Seselja ran a high-profile campaign last year for the ACT Legislative Assembly when he was ACT Opposition Leader.

The Greens campaigned hard on their desire to ''Abbott proof'' the Senate.