Two people were also injured when a 360-feet long section of the tunnel's concrete ceiling panels collapsed on to cars on Sunday morning along the Chuo Expressway in Yamanashi prefecture – 50 miles west of Tokyo.
"The Prime Minister ordered the Transport Ministry to put the utmost efforts into rescuing victims, to quickly investigate the cause of the accident and to establish measures to prevent similar accidents, and to provide a counselling service to victims to take care of them," Chief Cabinet Secretary Osamu Fujimura said.
The Land Ministry ordered highway companies with similar concrete panels in tunnels across the country to make emergency inspections.
An official from the highway operator, Central Nippon Expressway (Nexco), said the metal rods used to secure the concrete panels to the walls of the Sasago tunnel in the three-mile tunnel may have become loose.
"At this moment we're presuming that the top anchor bolts had come loose," Nexco said.
The ceiling panels had not been repaired or reinforced since they were built in 1977 but passed safety checks in September, public broadcaster NHK reported.
In 1996 a tunnel in Hokkaido, northern Japan, collapsed and falling rocks crushed cars and a bus, killing 20 people.