After voluntarily attending Sydney's Ryde police station he was arrested and subsequently charged by police.
The woman claims to have photographic evidence of the injuries sustained during the alleged assault.
The alleged incident occurred on September 30 in the NSW Hunter region.
A two-time Dally M Medallist, Hayne is one of the biggest names in the NRL.
He has played 11 Tests for Australia, 23 State of Origins for NSW and scored 121 tries in 214 NRL games.
7News reports Hayne has refused to answer any questions and charges are set to be laid.
After questioning by detectives from the sex crimes squad, Hayne was charged with aggravated sexual assault - inflicting actual bodily harm.
The claim likely comes as no help to Hayne's pursuit of a new NRL contract, after his most recent deal with Parramatta expired on October 31.
In 2015, Hayne was accused of sexual assault in America during his time with the 49ers.
The latest allegations come as Hayne faces civil legal action in the U.S. over claims he raped a woman during his time with the 49ers National Football League team in 2015.