Queensland University law professor Graeme Orr said the result would almost certainly go to the High Court, which could order the first re-run of an Australian Senate election in a century.
Orr said while there was a slim chance that the result changed, the ballots' disappearance affected the appearance of integrity.
The Sept. 7 election brought down a center-left Labor Party government and installed conservative Tony Abbott as prime minister.
In the initial results, the two tightly contested seats went to Palmer United Party candidate Zhenya Wang and Labor's Louise Pratt. But incumbent Greens Sen. Scott Ludham, who was set to lose his seat, requested a recount due to the close result.
The recount delivered the seats to Ludlam and Australian Sports Party candidate Wayne Dropulich. But the 1,375 ballots had disappeared before the recount.
Mining magnate Clive Palmer has demanded the first count stand, saying the missing ballots could have "already gone through the shredder."
That first count gave his fledgling Palmer's United Party a third Senate seat, making it an influential power bloc in the upper house.
Palmer, who won a seat in the House of Representatives, cautioned the AEC against declaring the result based on the recount.
"If they do that there'll certainly be a High Court challenge," Palmer told reporters.
Electoral Commissioner Ed Killesteyn has apologized for the missing ballots and announced an independent investigation.
The new senators are due to take their seats in July.