Officers from the Yamanashi Police Department entered the office of Central Nippon Expressway (Nexco) in Hachioji, western Tokyo.
A spokesman for the highway operator said it is fully cooperating with authorities.
Japanese broadcaster NHK says police also plan to raid more of the company's offices in connection with the tragedy at the Sasago tunnel, which passes through hills near Mount Fuji.
On Monday, the Japanese government ordered inspections of ageing highway tunnels following the accident as suspicion over the cause of the accident centred on decaying ceiling supports.
Two people were also injured when a 110 metre long section of the tunnel's concrete ceiling panels collapsed onto cars on Sunday morning along the Chuo Expressway in Yamanashi prefecture, about 80 kilometres 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 to make emergency inspections.
An official from Nexco said the metal rods used to secure the concrete panels to the walls in the 4.7 km tunnel may have become loose.
"At this moment we're presuming that the top anchor bolts had come loose," Nexco's Safety Service Center Chief Motohiro Takamisawa said.
The ceiling panels had not been repaired or reinforced since they were built in 1977, but passed safety checks in September, NHK reported.
In 1996 a tunnel in Hokkaido, northern Japan, collapsed and falling rocks crushed cars and a bus, killing 20 people.