IRRIGATOR groups have given cautious support to a new Murray Darling Basin water purchase program announced today.

The Federal Government announced today that the new water purchase program would being next week.

The Strategic Sub-system Reconfiguration Program will put deciding about water buy-backs into the hands of local infrastructure operators.

National Irrigators Council chief executive officer Tom Chesson said "at first blush" the program appeared to have merit.

"With over 80 per cent of the 1601 GL recovered to date having come through ad hoc buybacks the "Swiss cheese" effect on irrigation infrastructure schemes is a major issue,'' Mr Chesson said. 

"With the Government now wanting to recover up to 3200 GL it is hoped that future water recovery measures will not impact Infrastructure operators as severely as they have to date as a direct result of this program."

Water Minister Tony Burke said the program, to begin on February 18, formed part of the Government's response to the Windsor Inquiry.

He said the inquiry had concerns about the "so-called Swiss cheese effect where water purchases impacted on the efficiency and viability of shared irrigation networks".

He said irrigators and irrigation communities often complained about the Swiss cheese effect.

"They have consistently put the view that if buy-back does occur they should be strategic and not random," Mr Burke said.

"But the challenge has remained that there will be many different views on what actually constitutes a strategic purchase."

He said under the program, local infrastructure operators would lead the decisions.

"If some areas are to be reconfigured these decisions are made at the local level but the water recovered can contribute basin wide to the health of the Murray-Darling," Mr Burke said.

New South Wales Irrigators Council chief executive officer Andrew Gregson said previous schemes pitted irrigators against their service providers.

"We've consistently argued that the only way to make this happen properly is for agreement to be reached before government gets involved," Mr Gregson said.

"Any proposal needs to be made jointly by irrigators and service providers."

Funding of $200 million over four years was announced for this program in the 2012-13 Budget.

Meanwhile the Senate last week approved $1.7 billion to put an extra 450 gigalitres into the Murray-Darling Basin.

The 450GL takes the total amount to be recovered for the environment to 3200GL by 2024.

Mr Burke said that, without the now-passed legislation, the $1.7 billion could not be guaranteed.

He said the new funded account could be to recover water only if there was no social or economic downside for communities.

Proposed amendments by the Greens - to make 3200 gigalitres the minimum amount of water recovered, to recover the water by 2019 and to audit the amount of water returned to the system each year - were unsuccessful.