The federal coalition has told South Australian Premier Jay Weatherill to stop complaining about other states cutting their funding for the Murray-Darling Basin Authority.

The SA government plans to halve its funding for the authority to $14.3 million from July 2014, Fairfax Media said on Wednesday.

NSW has already cut its funding from $32 million to $12 million and will reduce it further to $8.9 million from July.

Federal opposition water spokesman Barnaby Joyce has accused Mr Weatherill of being "a complete and utter hypocrite" because SA has cut maintenance funding for basin infrastructure.

"If you are going to cut funding to the issue that is so important then don't complain to everybody else," Senator Joyce told reporters in Canberra on Wednesday.

People would ask how serious the premier was about funding basin programs, he said.

SA Liberal Senator Simon Birmingham says he has grave concerns about funding cuts by both NSW and his home state.

"It is obviously going to impede on the authority's ability to effectively manage the Murray Darling Basin and critically manage the water assets out there," he said.