Rescuers have found three more bodies in a collapsed tunnel on a major Japanese highway, taking the death toll to nine.

At least three vehicles were buried on Sunday when concrete ceiling panels crashed down inside the nearly five-kilometre tunnel which passes through hills near Mount Fuji, 80 kilometres west of Tokyo.

Witnesses spoke of terrifying scenes as at least one vehicle burst into flames inside one of Japan's longest road tunnels, sending out clouds of blinding, acrid smoke.

Five blackened bodies were found inside a single vehicle. Emergency workers also recovered the body of a truck driver, identified by broadcaster NHK as Tatsuya Nakagawa, 50, who had telephoned his company to ask for help.

Later, the bodies of an elderly man and two elderly women were recovered from a crushed vehicle in the Sasago tunnel on the Chuo Expressway, Kyodo News said.

Emergency workers equipped with breathing apparatus on Sunday battled around a third of the way into the tunnel, where they found 110 metres of concrete panels had fallen.

Hours later engineers warned the structure could be unstable, forcing rescuers to halt their work as a team of experts assessed the danger.

Dozens of people on Sunday abandoned their vehicles on the Tokyo-bound section of carriageway, and ran for the exits.