They believe the man might have entered the toilet on Friday night.
The restaurant was closed by workers at 10pm on Sunday, presumably with the man’s body in situ.
If it had been there since Friday, that would indicate the cubicle wasn’t checked or cleaned on Friday evening, all of Saturday when the store was open for 24 hours and Sunday.
The store manager would not comment and referred AAP to a Melbourne PR agency.
Hungry Jack’s refused to answer questions about cleaning arrangements at the restaurant and released a statement through the PR agency saying it was co-operating with all relevant authorities regarding the matter.
“Our thoughts are with all concerned,” it said.
The man’s death has not been deemed suspicious and might have been caused by a drug overdose.
Police are preparing a report for the coroner.
Stirling City Council health compliance officers were also investigating the death to make sure there was no public risk.
That included looking at whether health or sanitary issues needed to be addressed, a spokeswoman said.
Originally published as Body three days in Hungry Jack’s toilet