A Melbourne state high school says it has removed an online payment requirement for new enrolments, following criticism that it was charging non-refundable fees.

Cate Hall, the president of lobby group Our Children, Our Schools, said a member of the group was asked to pay $270 to enrol her child at Northcote High School in the city's north, despite government schools being obliged to provide free education to students.

"[The parent] noticed from the online form that you can't really proceed without giving over your credit card details and making this payment," Ms Hall said.

"She said it actually stated on that online form that it's non-refundable. This is concerning because obviously it should be free education.

"We understand that throughout the year there are certain fees for extras, but this was a non-refundable fee just for enrolling with no specific information about what the money is actually for.

"It's totally wrong. It's against what they should be doing."

The school's principal Kate Morris said the online payment requirement was not intentional and had been removed.

"Parents who enrolled their students for Year 7 at Northcote High School in 2016 will have noticed a message on the school's online enrolment portal," she said in a statement.

"This external portal, where the payment request can be actioned, was not intended to require upfront payment to secure a place for 2016.

"This payment requirement has now been removed by the school's external portal provider and parents can now complete the external online enrolment process without making a payment.

"The school will clarify the payment options in our next communication to families."

The claim has prompted the Education Department to issue a warning to all schools in Victoria.

The Education Department said it would write to all state schools in response to the claim to advise them they were legally obliged to provide free education.

It said it was not appropriate for government schools to request a payment to secure a place.

Education Minister James Merlino said he had ordered the department to check if any other schools were wrongly charging enrolment fees.

"It shouldn't have happened, the principal has apologised, the money is being reimbursed," he said.

"The department is making sure every single school across the state understands education is free and there is no down payment on enrolment."

Schools 'desperate' for money to make up funding shortfall

Ms Hall believed Northcote was not the only school asking for down payments.

She said the practice smacked of desperation from under-funded government schools.

"They know it's not quite right, but they're doing it anyway. You have to wonder if they're just grabbing money from wherever they can," she said.

"It is well known Victorian schools are underfunded per student compared to other states to the tune of about $2,000.

"There's also an oversight issue, a big picture issue. The auditor-general's report from not that long ago stated that the department doesn't really know how much it costs to run a school, and also the oversight to what's going on in schools with money.

"It's quite telling the department didn't know it was going on."

Ms Morris said Northcote High School was "approachable and flexible" and committed to meeting the needs of the community.

"A range of support options are available to parents who are experiencing financial difficulties," she said.