Police say the man's death is considered suspicious, and the Lower Mainland's Integrated Homicide Investigation Team has taken over the case.
Festival goer ReutAmit, who was camping across from the apparent crime scene, told CBC News a group of festival-goers discovered the man's body, and tried to keep others away until police arrive.
"Out tent is facing the Port-A-Potties, so we were sitting at our campsite and people were still using the washroom," she said. "It looked like a group of people were sort of blocking off this one Port-A-Potty and telling people not to go in."
"When police arrived, they cordoned off a small area at first.... And then, eventually, they cordoned off a much larger area and then the entire set of washrooms couldn't be used."
Police later brought in a trailer, and festival security told some of the campers that the area would remain cordoned-off all weekend.
Investigators said Saturday morning that they had not confirmed the cause of the man's death, or if it was foul play.
Homicide investigators also said they had confirmed the man's identity, but were withholding that information as his next-of-kin has yet to be notified.
IHIT said it would be providing more information to media and the public later on Saturday.
IHIT also issued a request through Twitter, asking festival-goers to get in touch with their families to let them know they are OK.
Festival organizers told CBC News they would be asking Pemberton Fire and Rescue to help campers near the possible crime scene in relocating their tents and belongings.
This year's Pemberton Music Festival features nearly 100 acts and predicted an attendance of 25,000 people.
The organizers from New Orleans, HUKA Entertainment, said they spent millions on improvements after a previous incarnation by another promoter in 2008 was marred by traffic jams, irritating dust and filthy portable toilets.