The Eden Killer Whale Museum was “very distressed” to learn that part of the collection was taken on March 27.
The museum confirmed the skull was located outside the gate to Eden Lookout early this morning.
The skull has been damaged over the last few months but the museum remains positive that it can feature in future exhibits.
It was being stored in a shed while the museum was undergoing renovations, rather than being on display, when it was taken.
At the time, the museum said that given the weight and size of the skull, large machinery such as a crane and flatbed truck would have been needed to move it.
NSW Police said they were investigating the incident at the time but have not confirmed the outcome of their inquiries.