Industry-run water efficiency projects are being audited, the Government claims.

Recent media investigations have raised questions about the use of a $4 billion fund set up to improve infrastructure on irrigation farms in exchange for water entitlements.

It suggested that farmer’s use of taxpayer money for water saving projects is not being audited.

Much of the investigation focused on the operations of Webster Limited, a big nut and cotton grower in the Murrumbidgee Valley.

The Federal Minister for Water Resources David Littleproud says audits do occur, and that he is confident the scheme has proper scrutiny.

“Water efficiency works are subject to risk-targeted spot audits by the federal Department of Agriculture, which has also had Deloitte carry out a separate audit”" Mr Littleproud said.

“The department began the process to audit Webster a few weeks ago. Delivery partners also check infrastructure works.”

The water efficiency scheme pays for projects put forth by farmers and big agriculture companies.

The National Farmers' Federation Water Taskforce chairman Les Gordon defended the industry’s involvement.

“Agriculture needs to have those bigger operators because often they've got the scale and the capital to introduce the new technologies, the new ways of doing things, so the rest of us can then adapt and adopt them into our practices,” he said.

“It's all part of that agricultural landscape.”

Mr Littleproud appears to agree.

“Some 95 per cent of the On Farm Irrigation Efficiency Program projects are worth less than $1 million, with an average project size of $152,000 across the 1,500 projects,” he said.

“These are almost all small projects involving small farmers, not big companies.”

The claims have reignited calls for a royal commission into the Murray-Darling Basin Plan.