Liberal candidate Gisele Kapterian has her nose ahead of independent Nicolette Boele in the northern Sydney electorate of Bradfield after the distribution of preferences.
Ms Boele had been declared the provisional winner before further counting flipped the standings.
Based on its policy for seats with a final margin of fewer than 100 votes, the Australian Electoral Commission will begin a recount on Monday.
The process will scrutinise more than 100,000 ballots and is expected to take two weeks.
"There have been three recounts in the last 20 years ... they don't happen very often," election analyst Ben Raue told AAP.
The most recent federal recount was in 2016 for the Queensland seat of Herbert, which Labor ultimately won by 37 votes.
Mining magnate Clive Palmer won Fairfax by 53 votes in 2013 after a recount lengthened by his scrutineers' challenging of votes.
Melbourne's McEwen was the subject of a dramatic to-and-fro in 2007.
Labor was ahead by seven votes after the initial count but the result switched to the Liberals by 12 following the recount.
Labor challenged the result in the court of disputed returns - a jurisdiction of the High Court that rules on the validity of elections - and ultimately won the seat.
Bradfield could go to a by-election if the recount returned similar numbers to the initial count or head to the dispute court if any parties challenged the outcome, Mr Raue said.
In another tight race, Labor is on track to pick up an extra seat in Melbourne's Calwell to add to its increased majority.
The seat has become a four-way contest between Labor, the Liberals, the Greens and an independent as the full preference distribution is carried out.
In the Senate, the electoral commission appeared to be close to "pushing the button" on the count to decide whether maverick Jacqui Lambie would be re-elected, Mr Raue said.
The Tasmanian is in a three-way battle for two Senate seats with veteran Liberal Richard Colbeck and Labor.
One Nation senator Malcolm Roberts is on track to reclaim his Queensland seat.
A win in Calwell would place the government on 94 seats in the 150-seat House of Representatives and cement its victory in every electorate held by Labor before the May 3 poll.
The Liberals have 28 seats in the lower house and the Nationals have 15.
The Greens have been reduced to one lower-house seat, with 11 shared between independents and other minor parties.
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