The woman claims to have photographs to back up her story.
It's understood she was interviewed by the NRL's integrity unit before the matter was referred to police.
"Police will allege in court that the man attended a home in the Hunter region on Sunday 30 September 2018, and sexually assaulted a 26-year-old woman," the statement read.
According to the Daily Telegraph, Hayne is banned from entering Newcastle and has surrendered his passport under strict bail conditions set following the charge.
It was reported Hayne declined to be formally interviewed.
After questioning by detectives from the sex crimes squad, Hayne was charged with aggravated sexual assault — inflicting actual bodily harm.
The charge carries a maximum 20-year jail term if Hayne is convicted. The NSW Criminal Code states for "circumstances of aggravation" means circumstances in which "the alleged offender intentionally or recklessly inflicts actual bodily harm on the alleged victim".
It's understood the alleged victim was interviewed by the NRL's integrity unit before the matter was referred to police.
A spokeswoman for NSW Police told news.com.au: "Police are investigating following reports a woman was sexually assaulted by a 30-year-old man in late September.
"The investigation is being led by detectives from the Child Abuse and Sex Crimes Squad."
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. The Eels had been hopeful at least one other player could be picked up by another club to fit Hayne into next year's salary cap.
"As this is a police matter the club will be making no public comment in relation to these reports," a Parramatta spokeswoman said.
Hayne's representative Wayne Beavis opted not to comment when contacted by AAP after the allegations arose.
A two-time Dally M Medallist, Hayne is one of the biggest names in the NRL thanks largely to his magical run to help Parramatta to the 2009 grand final. He has played 11 Tests for Australia and 23 State of Origins for NSW and scored 121 tries in 214 NRL games.
He also created headlines when he left the Eels to play in the NFL, running out for the San Francisco 49ers in late 2015.
However that one-year stay was plagued with drama, with Hayne still defending a civil court rape case made against him while living in the United States — an accusation he has long vehemently denied.
-with AAP