Suzanne Eaton, who went missing more than a week ago after going on a run, died of suffocation, police confirmed to the BBC.
They say they are investigating the case as a criminal act.
The 59-year-old molecular biologist from the world-renowned Max Planck Institute in Germany had been attending a conference on the island.
She was found on rough and rocky terrain inside the abandoned bunker about 10km (six miles) away from where she was last seen, according to police in the port city of Chania, where the conference was being held.
She was reported missing on 2 July and a large search effort was launched.
Six days later, her body was discovered by two locals exploring the bunker, which is a system of manmade caves used by the Nazis during the occupation of Crete in World War Two.