Hayne, 31, appeared briefly in the Newcastle Local Court on Wednesday before magistrate John Chicken.
Mr Chicken said he had not been "living in a bubble" and understood Hayne was facing a second aggravated sexual assault charge.
Defence lawyer Leo Premutico confirmed the new charge had been laid against Hayne and asked for two changes to his bail conditions, involving his residential address and where he would report to police.
Hayne, who is living in Queensland's Broadbeach Waters, is accused of sexually assaulting a 26-year-old woman on September 30, 2018, between 8pm and 10pm at Newcastle [Australian time].
Court documents state Hayne had sex with the woman without her consent and "recklessly inflicted actual bodily harm" to the woman during the alleged rape.
Mr Chicken agreed to vary Hayne's bail conditions and adjourned the matter to June 26.
Hayne did not speak to media as he was escorted by a police officer to a car waiting outside the courthouse.
Hayne's barrister has previously indicated in court that the former NRL player intends to plead not guilty.
The charges he faces each carry a maximum 20-year jail term.