Ms Mirabella had been gaining ground on her independent opponent Cathy McGowan as postal votes were counted on Wednesday, reducing the margin to just 500 votes.
But electoral officials noticed a disparity between the number of votes cast in the House of Representatives and the Senate in the Victorian seat of Indi and found a pile of 1003 votes favouring Ms McGowan had not been entered in the system.
The missing votes had been cast at a pre-poll centre in Wangaratta.
As of 6pm (AEST) on Wednesday, Ms McGowan was leading Ms Mirabella by 500 votes with more than 82 per cent of the vote counted, but the missing votes have not been added to the tally.
Victoria's closest contest, the seat of McEwen, has got even tighter.
Liberal candidate Donna Petrovich's lead over incumbent Rob Mitchell has been reduced to just 116 votes, with 78 per cent of the vote counted.
In 2007 the contest in McEwen took months to resolve and ended up in the Court of Dispute Returns.
Ms McGowan said it was possible that Indi could go the same way in 2013.
"I wouldn't be at all surprised if it did," she told AAP.
Ms McGowan found out about the extra votes on Twitter and described the discovery as "amazing".
"You wouldn't want it to be the other way, would you?" she said.
"It would be shocking."
Ms McGowan said it could be up to a week before the result was known, but she was enjoying the wait.
"I think that it has still got a bit of up and down to go before it gets sorted out," Ms McGowan said.
An AEC spokesman said the error was discovered as part of a number of checks and balances that take place during counting.
A spokesman for Ms Mirabella would not comment on the development, instead directing calls to Liberal Party headquarters.
Liberal Party state director Damien Mantach said there was no doubt the votes had given Ms McGowan a clear advantage in the count.
"Despite this turn of events, we're hopeful of making up ground with the thousands of votes that are still to be counted," he said in a statement.
ABC election analyst Antony Green said on Tuesday he expects Ms Mirabella will still get over the line.
Share
