The grim discovery - which is believed to be a man's body - was made on Sunday after police were called to the building, a former bank premises, in Batley.
Officers were forced to break into the building on Commercial Street after being called to the scene.
West Yorkshire Police has now confirmed it is investigating the incident as a murder and has said three people have been arrested over the murder.
The force released a statement on Tuesday morning saying: "The body, which is believed to be that of a man, was found inside the former bank premises in Commercial Street on Sunday, after officers forced entry to the building.
"Enquiries are continuing to confirm the identity of the deceased and the circumstances around the death.
"A scene remains in place at the location.
"Three people have been arrested on suspicion of conspiracy to murder. Two have been released under investigation while the third has been bailed."