Local media said the shock discovery was made at the Hungry Jack's outlet in a suburb of Perth on Monday morning, with the man thought to have entered the store some time on Friday.
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"Hungry Jack's is cooperating with all relevant authorities regarding the matter at its restaurant in Balga, Western Australia," the fast-food outlet said in a statement.
"Our thoughts are with all concerned."
Western Australian police gave no indication of how long the man had been dead before his body was discovered inside the locked cubicle.
"The death is not suspicious and a report will be prepared for the coroner," a police spokesperson told AFP.
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But the Australian Broadcasting Corporation said an investigation was underway to determine when he died in the stall which reportedly had a floor to ceiling door.
Reports said the store was open 24 hours on Saturdays and had closed for the weekend at 10pm on Sunday.
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