An investigation was launched by the Wildlife Crime Unit of Police Scotland after a member of the public found the bodies while walking in Bonnington Road, near Peebles, on Friday afternoon.
The badgers' pelts had been removed.
A Police Scotland spokesman said: "The remains of these animals will be forensically examined to try and determine how they died.
"We would urge anyone with information relevant to this enquiry to come forward.
"While we cannot confirm where the badgers died, at this time we would urge anyone who remembers seeing any suspicious activity in the Bonnington Road area to contact police."