A micro-party that is gunning for the final spot in the NSW upper house is likely to mount a legal challenge if it loses, potentially sending voters back to the ballot box.

The Animal Justice Party is battling it out with the No Land Tax Party, and the three major parties, for the last of 21 upper house seats being contested at Saturday's election.

However an early hiccup with the state's electronic voting system, iVote, saw AJP and another party left off the "above the line" section of the ballot paper.

About 19,000 votes were cast before iVote was suspended and the problem, which was due to human error, was fixed.

The Animal Justice Party lead candidate Mark Pearson told Fairfax Media on Monday that his party was "neck and neck" with the Liberal and No Land Tax parties for the remaining spot and preference flows "could get us over the line".

But he said the iVote error meant "we were not above the line for 36 hours".

"Most people do vote above the line and there's a measurable percentage of those people who really don't make up their mind until they go in and have a look [at the ballot paper]," Mr Pearson said.

Should the party not secure a spot "we'd seriously have to look at whether we go to the Supreme Court ??? to ask a judge to look at the issue and whether this election will be declared void", he said.

While the party was not keen to "drag people back to the polls", it wanted to be fair to those who voted for it, and those who "didn't have the advantage of seeing us over the line".

The NSW Electoral Commission has previously said even though two parties were temporarily left off part of the ballot paper, people could still vote for those parties below the line and "all votes were correctly recorded as per the voter's intention".

On Monday, a spokesman for the commission said any candidate can dispute the results of an election in the NSW Court of Disputed Returns.

About 66 per cent of the upper house votes had been counted by late on Monday.

It appeared the government had secured nine seats, Labor had seven and the Greens had snared two. The Christian Democratic Party and the Shooters and Fishers Party were expected to gain one seat each

The one undecided spot is not expected to be finalised for several weeks, after preferences are distributed.