A result in the knife-edge seat of Indi probably won't be known for another two weeks, according to the Australian Electoral Commission (AEC), with senior Coalition figure Sophie Mirabella now looking likely to face defeat.

An AEC spokesman told Guardian Australia the counting and scrutiny of about 15,000 postal and pre-poll votes means a further delay in the declaration of a result, with an automatic recount triggered if the difference between the two leading candidates is less than 100 votes. Earlier on Thursday, Mirabella ruled herself out of contention for the new Coalition ministry, despite having been shadow science minister in opposition. In a statement she said that due to the uncertainty over the Indi result, Tony Abbott would need to have "absolute freedom" to choose his frontbench team, which he is expected to announce on Monday.

Independent Cathy McGowan is currently 1,471 votes ahead of Mirabella. The incumbent appeared to be on course to overtake McGowan due to her clear majority among postal votes, until the dramatic discovery of 1,003 uncounted votes for McGowan.

Steve Kennedy, director of operations at the AEC, told the ABC the error was due to an "accounting problem".

"When [AEC staff] were doing the Wangaratta early voting centre, an anomaly in the tally sheet was found of around a thousand votes," he said.

"So the ballot papers have always been there with the other 6,000 ballot papers for that early voting centre, but there was a transposition/transcription error made on a bundle for candidate Cathy McGowan, the independent. It had 1,115: it should have been 2,115. So they weren't lost – they've always been there – it's just been incorrectly accounted for."

The unexpected addition of the votes has given McGowan's lead a cushion that many analysts expect cannot be overhauled by Mirabella.

A spokesman for McGowan's campaign told Guardian Australia: "It will be very close, but it's an uphill battle for Sophie now. These extra votes have made things a lot more comfortable."