The Dockers were returning to Western Australia on a charter service after going down to the Hawks in Launceston on July 13, when the incident unfolded and cabin crew were forced to scoop toilet waste into bins.
Transport Workers Union WA state secretary Tim Dawson said the issue resulted in non-functional toilets and an "unsafe environment" for all aboard.
"This situation is utterly unacceptable and demonstrates a glaring neglect of duty of care towards both our members and the passengers they serve," he said.
"Our cabin crew members should not be subjected to such hazardous working conditions and passengers should not have to endure such distressing experiences."
The situation reportedly forced cabin crew to manage the situation by manually scooping toilet waste into bins.
Passengers were also forced to use basins for urination, highlighting a severe breach of basic hygiene standards, according to the union.
The AFL has complained to the charter company and is awaiting the results of an investigation, league spokesman Jay Allen said.
"The AFL was left extremely disappointed after a charter flight from Launceston to Perth last weekend provided inadequate facilities for players, club staff and airline team members on board," he said.
"We thank staff and players from the Fremantle Football Club for their understanding and the airline staff on board for their professionalism during a difficult few hours in the air.
"Once the airline investigation is complete, we will work through next steps with the charter company."
A National Jet Express spokesperson said the incident was being taken "very seriously".
"NJE is aware of the situation on board a Launceston to Perth charter flight recently and is conducting a thorough investigation to ensure any failings are addressed immediately," the company said.
The unpleasantness followed an 87-74 loss to Hawthorn for the Dockers.
The AFL organises charter flights for clubs to get to and from interstate matches the quickest way possible.
