Former federal police commissioner Mick Keelty is already convinced the missing votes in the West Australian Senate election materially affected the result, but says it's unlikely their disappearance was caused by corruption.
He has also revealed electoral workers in other states have also alleged that the issue of disappearing votes has been commonplace for years.
Mr Keelty arrived in Perth on Monday to continue his inquiry into how electoral bosses lost 1370 votes for the September 7 federal poll from Bunbury East, Henley Brook, Mount Helena and Wundowie.
The modelling of the missing votes suggest the margin of victory in the senate could have been one vote, which would have been the closest result in the history of Senate elections.
Initial interviews carried out by Mr Keelty suggests the five boxes of missing ballots disappeared sometime between the day after the election and the recount beginning some weeks later.
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He has said while corruption was unlikely, it had not been ruled out.
"It is important we find out what went wrong ... fix those problems and make the future of the AEC's elections more accountable and with a better process of integrity," Mr Keelty said.
Early investigations have revealed that two separate losses of boxes may have occurred with batches of votes missing from Bunbury, two hours south of Perth, and Joondalup to the north of the CBD.
Examinations of how the thousands of boxes of votes were secured on pallets would be carried out.
The courier contracted to transport the votes, Toll will be quizzed as will various electoral officers.
Mr Keelty said he would also ask questions of another state's electoral commissioner about allegations votes could have been lost in previous elections.
"I have had emails sent to me by people working in other electoral commission officers around the country indicating to me these things are commonplace but they don't have such a big impact on the elections," Mr Keelty said.
Mr Keelty says he hopes to provide an interim report by the end of this month.
His inquiry will identify any administrative process or procedural failures that may have occurred, as well as providing findings and recommendations to the AEC.
The 1255 above-the-line ballots and 120 informal votes disappeared during a recount by the AEC after the election.
The Greens' Scott Ludlam and the Australian Sports Party's Wayne Dropulich claimed the seats which had been initially awarded to Labor's Louise Pratt and the Palmer United Party's (PUP) Zhenya Wang.
Mr Keelty has been allocated five Canberra-based AEC staff to assist his independent inquiry.
The AEC itself is still considering its position in relation to a possible petition to the Court of Disputed Returns.
Electoral commissioner Ed Killestyn conceded there was a "nagging and almost irreconcilable doubt" about the outcome.
Prime Minister Tony Abbott said he believed West Australians would welcome a fresh election - which would be the fourth time WA voters would have visited the polls in less 12 months if called.
