The body of the apparent stowaway was clad only in a long-sleeved, plaid shirt and jeans, police at Narita International Airport said.
A mechanic found the body lying inside the landing gear compartment of the Boeing 777-200 during maintenance after Delta Flight 59 landed Sunday night, police official Zenjiro Watanabe said.
"All we know is that he must have sneaked in just before departure, because it is impossible for him to enter the storage during flight," Watanabe said.
The man had no visible injuries except frostbite and may have died of hypothermia, Watanabe said. The temperature in that part of the plane falls to about minus 58 degrees during the long flight.
Police were investigating the case both as an accident and a possible crime, Watanabe said.
Delta officials were not immediately available for comment.
Similar cases have occurred in the past. In 2007, a man was found dead in the nose gear wheel well on a United Airlines flight that arrived in San Francisco from Shanghai. He, too, was thought to be a stowaway.