Concrete ceiling panels crushed cars and triggered the fire inside the nearly five-kilometre (three-mile) tunnel, 80 kilometres (50 miles) west of Tokyo.
Emergency workers had collected five charred bodies -- three men and two women -- from a vehicle by early Monday, Jiji said.
They had also recovered the body of a truck driver, according to the Fire and Disaster Management Agency.
He has been identified as 50-year-old Tatsuya Nakagawa, who contacted his firm immediately after the incident to ask for help, national broadcaster NHK said.
Three other deaths have been confirmed, an elderly man and two elderly women, who were all in the same passenger vehicle, Kyodo News said.
Local police officials in Yamanashi prefecture could not be reached for a immediate confirmation.
Footage from security cameras inside the tunnel showed large concrete panels that had apparently fallen from the ceiling with teams of men in protective gear scrambling over them.
Police had launched a negligence probe, Jiji said, while the operator of the highway said they found no abnormality during a regular inspection of the tunnel in September.