Momota, the world's top-ranked men's singles player, and three others were travelling in a hired van to the airport in Kuala Lumpur on Monday when it crashed into the back of a 30-tonne truck.
The van driver was killed while the four passengers were injured.
Momota, who won the Malaysia Masters on Sunday, suffered multiple lacerations to his face and a nasal bone fracture, the Badminton World Federation said.
Hospital Putrajaya, where Momota has been admitted, had no immediate comment.
Malaysia's Deputy Prime Minister Wan Azizah Wan Ismail visited the hospital and said Momota was stable.
"The doctors already said that the injuries they sustained can be healed and there was nothing serious," she said.
Momota is expected to be one of Japan's biggest hopes for gold at this year's Tokyo Olympics. (Reporting by Liz Lee; additional reporting by Lim Huey Teng and Ebrahim Harris; Editing by Peter Rutherford )