The federal water minister may top up a major drought rebate scheme that has run dry.

The $50 million On-farm Emergency Water Infrastructure Rebate Scheme covers 25 per cent of the bills for farmers to drill bores and desilt dams.

The scheme was meant to run for three years from 2018, but the money ran out earlier this year.

Many farmers had undertaken works that they assumed would be partly paid-for by the scheme, and are now left facing the full bill.

Federal Minister for Water Keith Pitt has blamed the states for running the scheme in such a way that farmers continued applying for the rebate after it had run dry.

“The Commonwealth has done exactly what it said it would,” Mr Pitt said.

“We've delivered our $50 million. I'm very much out looking to try and ensure we can help farmers out.

“We are talking around the October budget but, quite simply, this has been maladministration by the states.”

Queensland Agriculture Minister Mark Furner described the minister's criticism as “the worst kind of buck-passing”.

“The LNP should stop trying to have a go at Queensland's $745 million drought support to date — and actually open the Commonwealth wallet and support our farmers,” Mr Furner said.