The payment - $150 per year for primary and $250 for secondary school students - was available to disadvantaged parents to pay for school books, excursions, camps and computers.

At least one of the schools to lose the payment has sent out a letter notifying parents of the change and outlining a payment plan.

The plan involves parents making payments into their school account at any time, to be drawn upon when needed, instead of using the state government-provided payment.

Local principals met last week to discuss the changes and to create a consistent approach for all schools in Bendigo.

A principal of a local school, where 40 per cent of parents had previously received the payment, said plans would need to be put in place to cope with the changes.

"Forty per cent of families aren't going to receive the funding allowance," the principal, who chose not to be named, said.

"Our school is prepared to put in place payment plans to support our parents who had previously relied on this payment.

"We are also prepared to keep school fees at 2013 levels."

The principal said the school usually based its expenses around the EMA payment.

"It seems inequitable to us that 40 per cent of our families will not receive funding, while parents at the school down the road will continue to receive it."

The state government based its decision to remove the payment for certain schools on Student Family Occupation data.

Schools with parents with higher-earning professions had the payment removed.

All other schools would receive the payment directly to distribute to parents at their own discretion.

Golden Square Primary School retained a payment.

Principal Barry Goode said it was going to make it tougher for schools who would no longer receive the EMA.

"It's a shame to see changes in the structure in terms of the threshold," he said.

"Schools work really hard to always support their parents."

Education Minister Martin Dixon said the change gave more power to local principals.

"As a former school principal I know that school leaders understand the needs of their school community and this funding will give them certainty to plan for the 2015 school year," he said.

"This funding will assist disadvantaged families with education costs, such as uniforms, books and excursions, so that all students can fully participate in their education."