Politicians including Bob Katter, Trade Minister Steve Ciobo and Labor senator Sam Dastyari have failed multiple times to confirm they spent taxpayer money within the rules, according to Department of Finance lists.
But Prime Minister Malcolm Turnbull and Opposition Leader Bill Shorten have stopped short of demanding their party members catch up on all outstanding expenses.
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Health Minister stands aside pending investigation
Health Minister Sussan Ley steps down from the frontbench while she is investigated over her taxpayer-funded travel.
Since 2011 federal MPs have been asked each six months to sign a form promising their use of travel, accommodation and office entitlements was "in accordance with the parliamentary work expenses framework".
Health Minister Sussan Ley, who has stood down pending an investigation into her Gold Coast travel expenses, certified all her expenses as legitimate.
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But many politicians have missed batches and some are repeat offenders.
Queensland MP Bob Katter has never signed a certification form.
"It is not possible and would be very improper for him to sign a statement which sets out every single expenditure across his two offices when he is rarely in the offices," a spokeswoman for Mr Katter said when challenged in 2015.
While certification is voluntary, the man who advocated for the system, former Labor senator John Faulkner, thought public naming of those who failed to comply would be incentive enough.
"I certainly would not want to be a parliamentarian so named," Mr Faulkner told a Senate estimates committee in 2009.
And yet the former senator appeared as missing in two certifications - once in 2014 and once in 2015.
Minister for Trade, Tourism and Investment, Steve Ciobo - who missed periods in 2011, 2014 and 2016 - said he would need to check with a staff member why that was.
But he blasted certification as "incredibly bureaucratic" and "ridiculous" for asking politicians to verify purchases down to the level of office printer cartridges.
Mr Ciobo said when he did sign certifications it was always with the amendment: "to the best of my knowledge".
A spokesman for the Prime Minister said: "There are many legitimate reasons why a MP or Senator may not have certified their travel by the time the travel records are published."
"Most often it is because a MP or Senator is clarifying or querying the expenditure report."
Liberal MP Andrew Laming has missed four periods, as has Liberal senator Sean Edwards, according to the Department of Finance website. Labor MPs Michael Danby and Julie Owens as well as Senator Dastyari have each missed three.
A spokesman for Senator Dastyari, who resigned as a shadow minister over a donations scandal, said his office believed certification forms had already been supplied to the department but they had now been resubmitted.
Catherine King, the Labor health spokeswoman leading the political attacks on Ms Ley, was listed as missing two certifications in 2011 and 2013.
"We were of the genuine belief these had been certified," a spokeswoman for Ms King said. "We have checked with the Department of Finance and it appears to have been an oversight. This will be rectified today."
A Labor spokesperson said the government should "stop dragging their feet" and legislate to force all MPs to certify, as proposed by an independent review last March.
But Opposition Leader Bill Shorten would not say whether he would demand his MPs to verify all outstanding expenses.
Senator Nick Xenophon, who had not certified the last period, said he was "really annoyed" with himself, took full responsibility for the omission and would fix it as soon as he returned from Indonesia.
He said the expense list first submitted to him by the Department of Finance wrongly listed a business class flight.
As for parliamentarians who take an unreasonably long time to certify, Senator Xenophon said "there ought to be penalties".
Other former politicians listed as not having certified expenses include Joe Hockey, Phillip Ruddock, Andrew Robb, Bob Carr, Bob Brown, Craig Thomson and Clive Palmer.