Attempts to rescue those still trapped inside the smashed tunnel, which began spewing smoke after concrete ceiling panels fell onto the road, have been interrupted for fear they might trigger another collapse.
Three bodies have been found so far, television networks Fuji and Asahi said.
The fire service earlier said at least seven people were unaccounted for in the 4.7 km tunnel in Yamanashi prefecture, about 80 km west of Tokyo on the Chou Expressway, a main road connecting the capital to western Japan.
"Dense smoke was coming out as if it covers the entire mountain," witness Kiyoko Toyomura told Japanese news agency Kyodo.
The fire service said the blaze was extinguished about 11 a.m. - some three hours after the accident occurred.
The operator of the highway, Central Nippon Expressway, said a 50-60 metres long section of ceiling panels fell to the road, and it was looking into the cause of the accident.
Motorists described narrow escapes from falling debris, and a long walk through the darkness after abandoning their cars.
"When I was driving in the tunnel, concrete pieces fell down suddenly from the ceiling," a man in his 30s told public broadcaster NHK. "I saw a crushed car catching fire. I was frightened, left my car and walked for about an hour to get out of the tunnel."
In 1996 a tunnel in Hokkaido, northern Japan, collapsed and falling rocks crushed cars and a bus, killing 20 people.
NHK reporter Yoshio Goto, caught in Sunday's accident, hit the accelerator and managed to drive out.
"But it was a bit too late and pieces of ceiling fell on my car. I kept pressing the pedal and managed to get out," he said. "Then when I looked around, I saw half of the car ceiling was crushed."