Police were called to Auto Renovations, Rochester, Kent, by workers who had noticed a bad smell coming from the car's boot.
The dead man, thought to be in his late 20s or early 30s, could have been in the red Rover for some time, a police spokesman said.
Kent police confirmed the death is being treated as suspicious.
Paul Seymour, manager at Auto Renovations, said: "We were told by the finance people to pick the car up from an address in Dartford and bring it back to the yard.
"The finance people looked over the car and when they opened the boot there was a bad odour and they could see something bulky wrapped up, so shut the boot up and called the police.
"The nature of the job means that we do get cars that have been involved in crime, but a body is not an everyday occurrence."
Post mortem
Detective Chief Inspector Colin Murray said: "There was no clear physical indication of how he died. He was not shot, stabbed and there was no signs he had been beaten.
"We are awaiting the results of the toxicology tests but as yet there is no evidence to suggest it was drugs-related.
"The post mortem examination is inconclusive at the moment, and further tests need to be done."
An incident room has been set up at Dartford Police station and officers are concentrating their inquiries in the north Kent area.