The Griffith by-election in Brisbane will be used to test new security measures after the debacle of the WA Senate vote count in 2013.

New ways to secure ballot boxes and papers will be trialled at Saturday’s Griffith by-election to help avoid the errors of the Western Australian Senate election count in 2013.

The Australian Electoral Commission (AEC) faced a grilling at a Senate inquiry on Thursday over the flaws that led to 1370 ballot papers going missing in WA.

The inquiry heard that the commonwealth auditor-general had warned the commission at least four years ago about problems.

Last year’s WA debacle, for which the AEC has apologised, could lead to a fresh Senate election being run in that state and change the federal government’s prospects of getting laws passed.

An inquiry last year by former federal police chief Mick Keelty was inconclusive about how the ballot papers went missing during the WA Senate election recount, but made 32 recommendations.

Mr Keelty’s investigation revealed that ballot papers had been found in rubbish piles and ballot boxes had been unsealed without proper authority.

Acting electoral commissioner Tom Rogers told a Senate committee no one would ever know the fate of the missing ballot papers unless someone eventually came forward with them.

However, he said processes had been put in place for the Griffith by-election – to replace former prime minister Kevin Rudd – to prevent the error reoccurring.

These included police checks of staff, enhanced tracking and control of ballot papers, new security guidelines and improved materials management processes.

But Mr Rogers told the inquiry he could not give a guarantee errors would not occur.

“We’ve taken significant steps … (but) it doesn’t mean the steps we take will prevent a recurrence of that issue.”

His evidence came after Auditor-general Ian McPhee told the hearing the commission had been warned at least four years ago about problems.

Mr McPhee said his office had conducted audits of the commission’s processes in 2002, 2004 and 2010.

The most recent audit found the AEC needed to address the recruitment of suitable staff, reconciliation of ballot papers and the breaking of ballot box seals without witnesses.

The Senate committee heard that last year 60 per cent of election officials in WA were doing the job for the first time.

Brian Boyd, an Australian National Audit Office officer involved in the 2010 audit report into the AEC, told the inquiry the issue of ballot paper security was not merely academic.

“A changed result in one seat can change the government of the nation. It is more important now than ever,” he said.

Mr Rogers told the hearing he was surprised at the comments of the auditor-general as the audit office was represented on its business assurance committee and no issues had been raised in recent years.

Liberal MP and committee chairman Tony Smith said it was clear from the evidence there had been “alarm bells ringing”.

When Mr Smith asked whether it was the greatest failure in the history of the AEC, Mr Rogers said: “Indeed it is.”

But the acting commissioner added that the AEC had shown itself over many decades to be a “highly competent and trusted custodian” of federal elections whose skills in running elections were sought by other countries.

The inquiry continues.