The identity of the victim remains a mystery, but police will investigate cold cases and missing persons registers to identify the remains, with Sgt Fuhmeister unable to confirm the gender of the body or whether it is intact.
A black boot was the first sign to workers they'd made a gruesome discovery, after they'd been asked by the new storage facility owners to clean out the unit, which had not been accessed or paid for over many years.
The Herald Sun reports the shoe has been described as a "woman's boot" and that it "may be the breakthrough police need to solve a decades-old cold case".
"Jokingly, someone said it'd be freaky if there was a body in there. And we came across this, what looked like a boot, and someone said 'There's a boot'," Anton Hillemancher told the publication.
"I noticed what looked like a foot to me, in a sock, and I just thought, 'Oh, sh*t'."
Pictures show a large area sealed off by police tape. Several police vehicles are parked nearby and detectives were seen scouring through items inside.
"They found a wheelie bin inside there which was tied up with Occy straps and then they opened that up and found a boot in there and the boot was attached to a body," a worker told ABC TV.
Detective Senior Sergeant Pixie Fuhmeister told reporters at the scene the person had been dead for at least 15 years due to the level of decomposition.
"That container has not been accessed for a number of years," she said.
"We are determining the matter as suspicious at the moment and it is very early days and what we are looking at is long-term decomposition of the body."
Police expect to remain at the Milgate Street property on Saturday and will start searching lease records of storage containers, admitting a number of them have been abandoned for years.
The area remains cordoned off and bags of evidence have been removed from the scene.
The Herald Sun reports police are collecting CCTV from nearby businesses to determine how long the body may have been there before it was discovered.
A worker in the street told reporters the discovery was made after the business changed hands.
"The factory was recently sold and people cleaning it out today made the discovery," he said.
"They saw two legs sticking out and was told the body was there for five years."
The area where the remains were found is an industrial estate. Across the road is an F45 gym and a few streets away is the Huntingdale Primary School and Huntingdale golf club.
The body will be sent for forensic testing and police are urging anyone with information to call Crime Stoppers on 1800 333 000.
— With wires
