Father Roger Mount was rushed to Port Moresby General Hospital unconscious and vomiting on October 8, just hours after being made aware of plans to send him back to Australia.
Hospital and church officials said he has now been discharged and the ABC understands he is staying in Port Moresby while PNG immigration officials organise his deportation.
Father Mount has spent decades in Papua New Guinea, most recently at a small rural parish in Sogeri, 45 kilometres outside Port Moresby.
He is accused of sexually abusing boys in the 1960s while he was a brother at the St John of God-run home for intellectually disabled boys in Morisset, NSW.
Roger Mount has previously denied the allegations and has never faced charges, either in Australia or Papua New Guinea.
He refused an interview with the ABC at his PNG parish last week, saying he was waiting for a lawyer.
PNG's Catholic Church said the elderly priest ignored a suspension in 2011 and has overstayed his visa.
Alleged victim says Father 'laughed off' allegations
One of Father Roger Mount's alleged victims last week filed a complaint with police in New South Wales regarding allegations of abuse at the St John of God facility in the 1960s.
David McNamara received an apology and a $91,000 payout from St John of God in 1997, in response to allegations of abuse from three brothers, including Roger Mount.
Mr McNamara recently discovered that a non-disclosure agreement he had signed was not being upheld and decided to contact the Royal Commission into Institutional Responses to Child Sexual Abuse, as well as police.
"I went into Lismore police station and I made an official complaint," Mr McNamara said.
"They're going to interview me and send that interview down to the Lake Macquarie detectives because when you report stuff like this it goes back to where the abuse happened."
Mr McNamara said he would like to confront Father Mount in person about what happened in the 1960s, after an earlier conversation left him unsatisfied.
"I rang him up in 1991 ... in Papua New Guinea and I spoke to him and he remembered me," he said.
"He didn't deny anything, he just said, 'No, I couldn't remember' and laughed it off."