The woman who says she was raped by Jarryd Hayne deleted several messages regarding the former NRL star before handing her phone to police, a jury has heard.

As a criminal trial against Hayne, 35, continued on Wednesday, the officer-in-charge of investigating the alleged sexual assault was cross-examined by defence barrister Margaret Cunneen SC.

Ms Cunneen asked Detective Inspector Eugene Stek from the NSW Sex Crimes Squad about messages sent by the woman around the time of the alleged attack in late September 2018.

While she willingly gave her phone to police in November that year, the jury heard the complainant deleted “a large number of messages” before that date.

“Had she told you about that or not, sir?” Ms Cunneen asked.

“No,” Det Insp Stek replied.

These missing messages, which included 19 sent to Hayne, were either later uncovered by police during forensic analysis of her phone or revealed by Hayne’s legal team at his first trial in 2020.

On the same day as she did a walkthrough with police in early November 2018, the alleged victim also amended notes from her GP from an appointment days after the alleged sexual assault, the jury heard.

Hayne has pleaded not guilty to two counts of sexual intercourse without consent. He maintains that the sex was consensual and is facing his third trial over the allegations in the NSW District Court.

He attended the woman’s suburban Newcastle home after a friend’s bucks party on NRL grand final night in 2018.

The woman he is accused of performing non-consensual oral and digital sex upon cannot be identified.

It’s alleged he pulled the woman’s jeans off and performed the sex acts on her for about 30 seconds before she began to bleed.

Agreed facts filed with the court show Hayne did not consider the possibility that his actions would injure the complainant’s genitalia and that this was not his intention.

The matter was referred to the police by the NRL’s Integrity Unit in November that year.

The trial before Judge Graham Turnbull continues on Thursday.