The 33-year-old wrestler from Mongolia has already apologised and stepped down over the incident.
He is facing a summary indictment, which means he is expected to be fined rather than tried in court.
Japan’s sumo world has been hit by scandals involving violence, mafia links and match fixing in recent years.
Harumafuji’s assault on fellow Mongolian Takanoiwa happened while they were out drinking with other wrestlers in a bar in the western city of Tottori in October.
The grand champion is reported to have been angered that his countryman was checking his phone while being given advice. The latter was admitted to hospital with concussion and a fractured skull.
Harumafuji admitted punching him hitting him with a karaoke remote control but denied using a beer bottle in the attack.
“I’m truly sorry for hurting Takanoiwa mentally and physically,” Harumafuji told police, according to Jiji Press.
Harumafuji started his career in Japan at the age of 16 and was promoted to grand champion or yokozuna – sumo’s highest rank – in 2012.
The Japan Sumo Association (JSA) also recommended that its director Takanohana be demoted for failing to report the incident quickly enough, Kyodo news agency said.
Takanohana is a former sumo champion himself and the JSA is expected to finalise its decision in early January, according to Kyodo.