The audit is part of a US-brokered deal between presidential candidates Abdullah Abdullah and Ashraf Ghani, both of whom claim to have won the election designed to mark Afghanistan's first democratic transfer of power.
But Mr Abdullah's chief auditor Fazel Ahmad Manawi said: "The invalidation process is just a joke and there is no intention of throwing out fraudulent votes. If our demands are not accepted by tomorrow morning, we will not continue with this process, and any outcome will have no value to us."
Mr Abdullah led after a first-round vote in April but failed to secure an outright majority.
He trailed behind Mr Ghani in a June run-off, according to preliminary figures, and has since rejected the outcome, claiming widespread vote rigging.
As part of a plan to end the dispute, the Independent Election Commission is meant to throw out ballots deemed fraudulent in an audit of all eight million votes cast.
Tension over the outcome of the vote has raised the spectre of another civil war in Afghanistan after the country was torn apart by years of fighting in the 1990s, which eventually led to the rise to power of the Taliban.
"Whatever consequences are going to follow, we will not be responsible," Mr Manawi said, adding the UN was aware of their complaints but had failed to address them properly.
Afghanistan's Western allies are hoping a new leader will be in place before September 4, when a Nato summit is due to be held in south Wales.
Countries at the summit will weigh how much aid Afghanistan will get after most foreign troops pull out at the end of this year.
A peaceful transfer of power would allow the US and Afghanistan's other Western allies to trumpet a degree of success.