The nearly 1,400 Senate ballot slips that disappeared in Western Australia during the last federal election may have literally fallen off the back of a truck, says a federal parliamentary committee.

The Joint Standing Committee on Electoral Matters lambasted the Australian Electoral Commission (AEC) in its final report into the 2013 federal election, describing the incident as "disastrous".

The inquiry handed down 24 recommendations, including that voters be required to show identification and — for the first time in almost a century — vote using a pen.

It described the loss of the 1,370 ballots as "the greatest failure in the history of the Australian Electoral Commission".

The missing votes triggered a $21-million re-run of the Senate election in WA, which the committee said caused unprecedented damage to the reputation of and confidence in the AEC.

The committee found ballot slips were transported to the counting centre in Perth in the back of an open truck.

It suggested if the votes did not physically fall out of the back of the truck, it was possible they may have been mistaken for rubbish after being stored next to piles of discarded boxes.

The committee also found there were times when the counting centre was not secure, such as when a roller door was left open to allow fresh air to flow in.

The report cites an investigation by former AFP Commissioner Mick Keelty, who said it was impossible to determine what happened to the votes but suggests they could have been physically removed or lost during transport, accidentally disposed of or misplaced into incorrect boxes.

The committee attributed the incident to "multiple failures at multiple levels within the AEC" at both a state and federal level.

Electoral Commissioner Ed Killesteyn and the AEC's WA manager Peter Kramer resigned in the wake of the votes disappearing.

The report handed down 24 recommendations to the AEC including the strengthening of accountability of state manager positions, the development of key performance indicators for senior service delivery staff, and the development of a corporate culture, leadership and performance measurement reform.

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