No bodies were being stored in the premises of Colin Sneddon Funeral Directors, at Woodend Industrial Estate in Cowdenbeath, Fife, at the time.
The outside door was kicked in, as was the internal door for the mortuary in what is thought to be a pre-meditated break in.
An alarm went off, and a nearby resident allegedly saw two men fleeing from the estate and leaving in a car.
Funeral director Colin Sneddon said: "It just shows you how depraved some people can be.
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"I got a call from police at around 12.30am, to say that there had been a break-in. I was really shocked and disgusted.
"The alarm went off right on 12, for the bells.
"There were lots of fireworks going on at that time so they may have done it then so the alarm wasn't heard. There's nothing in the mortuary to steal.
"There weren't any deceased there.
"It looks like it was just opportunists to see what was in my unit as I don't have signage, so they wouldn't know what was in there.
He added: "I've since been told that a resident who lives opposite heard the alarm going off and they saw two men running out and into a car."
The damage is expected to cost around £100,000.
A Police Scotland spokesperson said: "Officers received report of a break-in to a premises on Station Road in Cowdenbeath around 12.05am on Saturday, January,1. Enquiries are ongoing."