GOULBURN Murray Irrigation District irrigators are set to lose a large share of water savings owed to them under the $1 billion Northern Victoria Irrigation Renewal Project.

That's the warning from Victorian Water Minister Tim Holding, who says the Coalition and Greens are blocking bulk entitlement amendments crucial to the storage and allocation of NVIRP water savings to irrigators.

Under the scheme, a third of the water savings recovered in 2010-11 from the project is due to be returned to GMID irrigators, with the remainder split between Melbourne and the environment.

However, the Coalition has disallowed the bulk entitlement amendments to the Goulburn and has declared it will block further Government attempts to amend the Murray and Goulburn bulk entitlements.

The Government is able to sidestep the Coalition's disallowance motions to supply water savings to Melbourne and the environment by using "Supply by Agreement" arrangements.

But Mr Holding said it was not feasible to draft similar agreements for thousands of GMID irrigators, who are contributing $100 million to the $1 billion stage one NVIRP scheme.

Without some means of storing and quarantining the water savings, Goulburn Murray Water will be forced to allocate the savings to all water users across northern Victoria, including the Commonwealth, private diverters, towns and Sunraysia irrigators. Up to 54 per cent of the water savings on the Murray system will be diverted to water users outside the GMID.

On the Goulburn, about 20 per cent of the savings may be lost to water users outside the Goulburn Districts, the Government warns.

But Coalition rural water spokesman Peter Walsh said the Coalition would not pass the bulk entitlement amendments until they reflected the Government's promise to share the water savings from stage two of the NVIRP equally between irrigators and the environment.

Mr Walsh said the Coalition also rejected the Government's attempts to use the bulk entitlement amendment to give Melbourne Water retailers access to north-south pipeline water outside the irrigation season.