The driver was killed at the scene after the vehicle collided with a slow-moving lorry on a highway. An assistant coach, physiotherapist, and badminton official also suffered minor injuries.
The accident came after the dominant Japanese star began his 2020 season in style Sunday with victory over Denmark's Viktor Axelsen in Kuala Lumpur.
"It's truly tragic, especially involving a badminton icon like Momota," Malaysian sports minister Syed Saddiq told reporters, after visiting the injured in hospital south of the capital. But he added those hurt were "recovering well, (and) all four are also in stable condition".
The others hurt suffered facial, leg, hand and head injuries, according to the police.
The Badminton Association of Malaysia said in a statement they were "saddened" by the crash.
The accident happened around 4:40 am (2040 GMT Sunday), and 10 firefighters rushed to the scene, senior fire and rescue department official Norazam Khamis told AFP.
The injured "were able to walk out of the van by themselves with some scratches", he added. Pictures showed the front of the van crushed against a lorry but the back section appeared intact.