THE AFL says it is "extremely disappointed" a four-hour flight carrying Fremantle players and staff ran out of water 30 minutes after take off, which left passengers without working toilet facilities.
The Dockers were travelling back to Perth on a chartered flight after their loss to Hawthorn in Launceston last weekend when the incident unfolded.
The WA Transport Workers Union said the situation forced cabin crew to manage the situation by manually scooping toilet waste into basins.
This led to passengers being forced to use basins for urination, highlighting a severe breach of basic hygiene standards, the union said.
The AFL condemned the incident and said it will wait for the results of the charter company's investigation.
"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," AFL spokesperson Jay Allen said.
"We have expressed this directly with the charter company and are awaiting the results of their investigation.
"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."
The Transport Workers Union's WA state secretary Tim Dawson said the issue resulted in non-functional toilets and an "unsafe environment" for crew and passengers.
"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."
A National Jet Express spokesperson said the incident is 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 into the incident to ensure any failings are addressed immediately," the company said.
While clubs mostly travel to interstate games via the AFL's partner airline Virgin Australia, the League does organise charter flights for some routes in order to get players and staff to and from games as quickly as possible.