But Federal Education Minister Dan Tehan says the offer, which would give independent and Catholic schools early payment of annual funding, aligns with Commonwealth health experts' advice.

Mr Tehan says funding for the schools will only be advanced if 50 per cent of a school's students return to classrooms by June 1.

It comes as the state government has maintained its decision for students to learn remotely for term two, based on advice from Victorian Chief Health Officer Brett Sutton.

Warrnambool King's College principal Allister Rouse said the incentive presented schools with an unfair decision.

"It is a health issue over a monetary issue and that's the big issue I see, they are putting finance ahead of the well being of staff and students," Mr Rouse said.

Mr Rouse said the school's leadership was yet to decide its next course of action.

"Regardless of if we accept the offer or not, the school will be working on a plan to return to full onsite learning, but when that will be is yet to be determined," he said.

"I would image that would be a scaled return by year levels, a winding back of the things we put in place."

But Mr Rouse said the federal government announcement had the outcome of "playing sectors against one another".

"In a local context it's more about the perception that presents in the community," he said.

"The four secondary school schools have worked really well to be consistent in how we manage educational issues."

St Joseph's Primary School principal Michael Gray said the school would continue to follow the advice of the Catholic school authorities and the Victoria government.

"The advice on teaching and learning comes from the state education department," Mr Gray said.

He added that the school was keen to "move from this unsettled time to a more normal school life".

Mr Tehan told The Standard if schools were to take the incentive they wouldn't be going against expert health advice.

"It's not going against the advice of the state government, what they can do is act consistently with the (Commonwealth's) medical panel, which includes the Victorian Chief Medical Officer, and what their board or diocese has to say," Mr Tehan said.

"Their advice has been clear that it's safe for students to go to school and teachers to be at school as long as proper protocols are put in place."

Mr Tehan said his own children had been attending school classrooms while learning remotely.

"One is boarding and the other tried going to school for term two doing supervised learning," he said. "She thought it was important to do that because I have been pushing to get schools back."

Mr Tehan said the Victorian government had taken a "very cautionary approach" but he didn't want parents choosing between going to work and supervising their children, or at-risk students falling further behind.

"We don't want those students disengaging from the classrooms because if they do all the research says their literary and numeracy will suffer," he said.

Victorian Education Minister James Merlino on Wednesday labelled any Victorian school that chose not to follow the state's health advice "reckless".

"What the federal government is doing is using funding to force non-government schools to ignore the expert health advice of Victoria's health officer," Mr Merlino told reporters.

"Now is not the time to change the course that we are on, a course that is making a difference."

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