Harumafuji's apology came after local media reported he had beaten junior wrestler Takanoiwa during a drinking session with other wrestlers, says a BBC report.
Takanoiwa had to be hospitalised after suffering a concussion and a fractured skull base in the incident, local media reported.
A spokesperson for Japan's Sumo Association (JSA) said Harumafuji's coach Isegahama had told the JSA on Wednesday of the wrestler's decision to quit.
At a Monday press conference, a speaker for an advisory body to the JSA had said the case required "extremely harsh punishment" but that no final decision had been made yet.
"There is almost no doubting that an act of violence was carried out," he said.
The incident follows a string of similar scandals and reports of violence.
In 2016, a wrestler and his coach had to pay nearly $300,000 (£230,000) to a fellow fighter they allegedly abused so badly he lost sight in one eye, according to reports.
Thirteen senior wrestlers were implicated in a match fixing scandal in 2011 while a year earlier, the sport was rocked by alleged links between sumo wrestlers and the mafia-like yakuza crime syndicates.
Another Mongolian grand champion retired from the sport in 2010 after reports of his involvement in a drunken brawl.
In 2007, a teenage novice died after he was beaten up by older wrestlers in a case exposing a culture of bullying and hazing within the traditional sport's strict hierarchy.
