THE body upgrading northern Victoria's irrigation system has been accused of wasting money on checking risks to Aboriginal heritage.

The Northern Victoria Irrigation Renewal Project is required to develop cultural heritage management plans for works that result in major soil disturbance.

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NVIRP's obligations under the Aboriginal Heritage Act have seen it pay for risk assessments for on-ground works to identify when a management plan is required.

But the Victorian Farmers Federation claims it is "ludicrous" that NVIRP is spending public funds on assessing the risk of replacing Dethridge wheels.

VFF water council chairman Richard Anderson said it was "overkill" to pay consultants to check whether wheel replacement could disturb Aboriginal remains.

"To me the whole thing is ridiculous," Mr Anderson said.

"It just seems ludicrous - any chance of any archeological remains would have been well and truly destroyed by now."

Victorian Nationals deputy leader Peter Walsh said it was "totally illogical" to spend money on assessing the risk of replacing Dethridge wheels.

"A realignment of a channel may be different but it is a complete waste of taxpayers' money when it comes to Dethridge wheels," Mr Walsh said.

NVIRP modernisation manager David Kent dismissed the claims.

Mr Kent said NVIRP was required by law to ensure the project did not damage Aboriginal heritage.

"With a project of this size we have to make sure we do everything appropriately and tick all the boxes (so) I don't think we are wasting money at all," Mr Kent said.

He said NVIRP obtained initial risk assessments from the irrigation designers it employed to work with farmers on farm re-design.

"If we accept there is minimal risk (to Aboriginal heritage) we will just go and replace the outlet," he said.

A spokeswoman earlier confirmed NVIRP considered it necessary to assess threats posed by replacing Dethridge wheels to Aboriginal heritage.

"As with the rest of the project, NVIRP applies a risk-based assessment to Dethridge wheel replacement," the spokeswoman said.

She declined to say how many risk assessments had been carried out on replacing Dethridge wheels. She also declined to say how much money was being spent on the checks.

Earlier this year it emerged that less than 80 per cent of the $1 billion earmarked for stage one of NVIRP was being spent on the ground.