MELBOURNE has found a fair chunk of water for its north-south pipeline - in the parched Wimmera Mallee.

The Weekly Times can reveal the Victorian Government will divert 12,000 megalitres of water that had been flowing to the state's northwest and send it down the controversial pipeline.

The savings are part of 64,000 megalitres earmarked for Melbourne next year, half of which will be available before June 30.

The first 32,000 megalitres have already been reserved in Lake Eildon, to await completion of the north-south pipeline early next year.

This parcel includes the 12,000 megalitres traditionally supplied to the Wimmera Mallee region from the Goulburn Murray Irrigation District, via the Waranga Western Channel.

The Government has used its legislative powers to take the water, which is deemed no longer necessary for Wimmera Mallee farmers and towns, given they are being supplied with water from the $688 million Grampians Wimmera Mallee pipeline network.

The 12,000 megalitres freed up from the 9000km pipeline works was earmarked to boost Loddon, Goulburn and Murray River flows.

But Water Minister Tim Holding secreted the water away for Melbourne on June 28 using his powers to "qualify" water rights.

The move is certain to outrage green groups, given the water was ultimately destined to revive ailing rivers.

But Victorian Farmers Federation water council chairman Richard Anderson said irrigators really didn't have any claim on the water, given it was earmarked for the environment once the Wimmera Mallee pipeline was completed.

Mr Holding's June 28 letter qualifying rights states Goulburn Murray Water's: "obligation ... to supply up to 24,000 megalitres to Grampians Wimmera Mallee Rural Water Corporation in every second year, and up to 2000 megalitres every year, is suspended ... "

The letter goes on to say this water "must be reserved for the purpose of urban supply requirements that may be necessary under continuing dry conditions".

A key Victorian Government source said the water had been set aside for Melbourne, but a deal had been struck to limit Melbourne's take to 12,000 megalitres based on historic usage.

The Government source said the first 32,000 megalitres to flow down the north-south pipeline before June 30 next year included 12,000 megalitres from the Wimmera Mallee, 10,000 megalitres from Lake Eildon's water quality reserve and 10,000 megalitres saved from irrigation modernisation works in the Goulburn Murray Irrigation District last season (due to be audited next month).

Another 32,000 megalitres has been earmarked for Melbourne for delivery after June 30, consisting of 20,000 megalitres of estimated water savings from the Goulburn Murray irrigation modernisation works, 10,000 megalitres from Eildon's water quality reserve and another 2000 megalitres earmarked for the Wimmera Mallee.

The 20,000 megalitre parcel of "estimated" water savings came under fire from irrigators last week, who argued it should have been allocated to irrigators, not set aside for Melbourne.

Mr Anderson called on the Government to ensure the savings were independently audited before one drop went down the pipeline.

Nationals water spokesman Peter Walsh last week accused the Government of stealing 40,000 megalitres from irrigators.

"Changes to the breakdown of water stored in the Goulburn system made between August 17 and September 1 on GMW's website show the authority increased the volume of water reserved for urban and environmental use by 40 billion litres (40,000 megalitres)," Mr Walsh said.

"The additional water, likely to be reserved entirely for Melbourne through the north-south pipeline, is the main reason why water allocations to irrigators have been set at zero for this season."

However GMW Water Resources manager Graeme Hannan said "the requirement for GMW to restore environmental flows in the Goulburn River accounted for a significant proportion of the 40,000 megalitres.

The Weekly Times understands about 20,000 megalitres of the 40,000 is required to maintain environmental flows on the Goulburn River.

GMW was forced to estimate the 20,000 megalitres of savings for this season, but will not be allowed to deliver the water to Melbourne until they have been audited at the end in May next year.