Efforts to rescue any survivors trapped inside the tunnel were hindered by heavy smoke after one vehicle caught fire inside the Sasago Tunnel, about 80 kilometers (50 miles) outside Tokyo.
Rescuers also temporarily suspended work because of fears of a further collapse. They were attempting to reach at least several vehicles believed buried in the rubble, including a truck whose driver was trapped inside and had called his company for help.
"I could hear voices of people calling for help, but the fire was just too strong," said a woman interviewed by public broadcaster NHK after she escaped from the tunnel.
The Fire and Disaster Management Agency issued a statement late Sunday saying five people were confirmed to have been in a car that burned inside the tunnel, and at least one other was in a truck. However, officials said they could not confirm the exact number of people believed dead.
Executives for Central Japan Expressway Co. said the company was investigating why the concrete panels had given way. A check of the 4.7-kilometer (3-mile) tunnel's roof in September and October found nothing amiss, they said.
It said two people were confirmed hurt, but the injuries were not severe.
The tunnel, which opened in 1977, is one of many in mountainous Japan. The location of the collapse, about 1.7 kilometers (a mile) inside the tunnel, was complicating rescue efforts, reports said.
Police vehicles, fire trucks and ambulances were massed outside the tunnel's entrance.