Commission spokesman Phil Diak says an exhaustive search has been conducted, including of all premises where Senate votes were stored, and it appears they will not turn up.
He says there is nothing to suggest anything improper has occurred but the AEC has called in former Australian Federal Police commissioner Mick Keelty to conduct an independent investigation.
"I don't think you should prejudge where the investigation is going to land," Diak told ABC radio.
Missing are 1255 formal votes and 120 informal votes from the electorates of Pearce and Forrest which could not be found for the recount.
The recount was called because of the close count for the sixth Senate seat between Greens Senator Scott Ludlam and Palmer United Party candidate Dio Wang, who won in the initial count.
Even without those votes, the AEC is expected to declare the Senate result soon.
Independent senator Nick Xenophon paraphrased Oscar Wilde.
"To lose one vote is unfortunate, to lose two is careless but to lose 1375 votes surely must be cause for a fresh Senate election," he told ABC radio.