The victim, who has not yet been named, was part of a team of five contractors at the Parkmore Distillery in Dufftown when he fell through the roof.
Police were called to the site at around 11.40am on Tuesday.
Built in 1894, whisky production ceased in 1931 because of problems with its water source.
Maltings at the site continued until the 1960s but now only the warehouses are currently in use.
They are used by whisky giants Edrington whose brands include Macallan, The Famous Grouse, Cutty Sark and Highland Park.
A spokesman for Police Scotland said: “Officers were made aware of the death of a male at around 11.40am yesterday.
“There are no apparent suspicious circumstances and inquiries are ongoing to find out the full set of circumstances surrounding the death.”
A spokesman for Edrington said: “We can confirm that there was a serious incident at the Parkmore warehouses near Dufftown yesterday morning in which a building contractor died.
“The man has not yet been named by police.
“Emergency services were called immediately, but the man died at the scene. No one else was hurt.
“We are shocked and saddened by this tragic incident and our thoughts and sincere sympathies are with the man’s family.
“The safety of our employees and the contractors who work with us is paramount to Edrington and we are cooperating fully with the relevant authorities as they continue their investigations.”
A Dufftown resident, who didn’t want to be named, said: “I was walking past the distillery and saw some police outside and wondered what was going on.
“Then somebody told me that a guy had fallen through the roof.
“The Parkmore has been shut for years and years and I don’t even think anybody works there directly now.
“I think they just get people to watch over it sometimes and move barrels about the warehouse.
“It’s really terrible, it’s such a shock to hear about accidents like this so close.”