The union watchdog is trying to piece together shredded documents as part of a controversial donations investigation.
The Registered Organisations Commission, which also regulates employer associations, is pushing ahead with a probe into the Australian Workers' Union.
Commissioner Mark Bilecki said a court last year overturned a ruling the investigation was invalid despite the union alleging it was politically motivated.
ROC-initiated Australian Federal Police raids on AWU offices in 2017 sparked controversy and years of legal action after media was tipped off.
"We have now obtained the disputed documents from the AFP including shredded documents that were seized during the execution of search warrants," Mr Bilecki told a Senate hearing on Wednesday.
ROC executive director Chris Enright confirmed there was two to three shopping bags of shredded documents.
The investigation centres on whether donations from the AWU to Labor candidates and GetUp were properly authorised when Bill Shorten led the union.
The investigation relates to donations of $100,000 to GetUp and of $131,500 paid to the ALP ahead of the 2007 election.
Mr Shorten insists all donations made before he entered parliament in 2007 were above board.
Liberal senator Eric Abetz said the ROC acted wisely in seeking a warrant on the basis documents could be destroyed.
"Good luck trying to put the shredded documents back together but one can only wonder what may have motivated the shredding," he said.
"It might give us an insight as to why the venom was poured out against the ROC and individuals in the ROC, and why so much money was spent on court proceedings."
Labor senator Tony Sheldon asked the two ROC officials, senior bureaucrat Martin Hehir and government minister Jonathon Duniam to confirm they also shredded documents.
"There is normal document disposal on every day," Senator Sheldon said.
"It does not mean that documents that any of these four people or anyone else have disposed of are relevant to any case unless you have proved it."
Nationals senator Perin Davey said there was a difference between shredding documents in day-to-day operations and doing so while under investigation.
After last year's court ruling, the AWU left the possibility of going to the High Court open.