Mark Northam, the assistant secretary and spokesperson for the Independent Education Union of Australia, confirmed on Wednesday that representatives have been "providing support over a number of weeks".

"We're aware [of the resignation], it's an enormously complex situation," Mr Northam told The Daily Advertiser.

"It's something we need to wrap our heads around.

"The union may be able to comment further next week."

It is understood Lyn Caton, the organiser of the NSW/ACT branch of the union, has visited Wagga this week to continue discussions with the school.

Mr Whelan's sudden withdrawal from the school after six years at the helm sent shockwaves through the school community.

After a lifetime's involvement with the school, Stephen Lawler has made the decision to remove his year 12 son from the school.

"My daughter went to that school, my son's been there right the way through, my wife went there and basically my whole family have gone there," said the 53-year-old father.

"In all my years with Catholic education, I've never seen anything like this at all."

Following an alleged confrontation with a member of the Catholic Education Diocese of Wagga Wagga, Mr Lawler made the decision to cut ties with the school.

"It's a completely different school to what it was two weeks ago, you wouldn't even recognise it any more," he said.

"I just didn't want to leave my son in that hostile environment."

Having removed his son on Wednesday morning, Mr Lawler called around to various schools to begin re-enrolment. But proximity to the HSC has caused significant headache.

"Right now I've got a son at home who's meant to sit his HSC in three weeks, but I don't know where or if he's going to do that," he said.

"I'm not sure where my son is going to school tomorrow."

The development has come at the worse possible time for Mr Lawler and his family, with him due to travel to Sydney next week for major surgery following a workplace accident.

"This is the last thing I need, but what am I meant to do? What is any parent meant to do? It's just all blown up in about 10 seconds it seems," Mr Lawler said.

"Every dealing I've ever had with the school has been upstanding until now."

Mark MacLean, the director of schools at the Catholic Education Diocese of Wagga Wagga, announced on Friday afternoon that Mr Whelan would not be returning to the school after commencing a period of leave effective from August 14.