A parliamentary committee is seeking a legal change so ballot papers in unlawfully handled ballot boxes may still be counted in an election.

The change was sparked by an inquiry, headed by former electoral commissioner Bill Gray, into problems with ballot papers in the seats of Boothby in South Australia and Flynn in Queensland at the 2010 election.

The problems led to a total of 4283 pre-poll votes being excluded in the two seats - not enough votes to change the results in either seat.

In Boothby, at the close of each pre-poll voting day before the August 21 election, the officer in charge at the Oaklands Park booth opened small ballot boxes for what the officer described as an "end-of-day amalgamation of papers".

The ballot papers were then cross-checked with stubs and put into two larger boxes for the lower house and Senate, sealed and locked in a room.

On election night, an ALP scrutineer noticed that the lower house ballot papers were all "stacked and flat" and the Senate papers were "disordered and jumbled".

The scrutineer reported his concerns on the Monday after the election, and the electoral commission concluded that the "irregular opening" of the boxes meant the ballot papers should be excluded.

The AEC said that reduced the lead of Liberal MP Andrew Southcott by 339 votes.

The officer in charge said in his defence that he was unaware the opening of the boxes was illegal and he was "remorseful and embarrassed".

But there was no evidence of ballot paper tampering.

In the seat of Flynn, the officer in charge at Blackwater broke open the seals on a ballot box the night before the election and "unwittingly breached" the Electoral Act.

The box was reported and quarantined, and the AEC decided that 452 early votes would not be included in the count.

An officer in nearby Emerald also was found to have, on three occasions, opened a ballot box to "rearrange the papers and create more space".

A total of 854 ordinary pre-poll votes were excluded from the count.

The parliamentary electoral matters committee said in its report on electoral law changes that votes should be reinstated "if ballot boxes are handled unlawfully but ballot papers are not tampered with".

The committee also recommended that the penalties for unlawfully tampering with a ballot box or ballot papers be clarified.

"The committee's view is that this balances voter enfranchisement and electoral integrity," committee chairman Daryl Melham said in a statement on Friday.

Opposition members on the committee agreed with the proposal, but argued the ballot boxes in question should be kept separate and the seat's returning officer be empowered to decide on the exclusion of votes.

The report also recommended better training for voting officers