South Australia's royal commission into the Murray-Darling river system has confirmed it will not investigate water theft cases or New South Wales bureaucrats already under investigation or prosecution by other bodies such as the New South Wales ICAC.

The former Weatherill government launched the royal commission last year, in the wake of allegations of upstream water theft first aired on Four Corners.

At the time, the then-premier said the state royal commission would have the powers to compel bureaucrats from interstate to give evidence.

"And they will have no choice but to come forward," Mr Weatherill said.

"A state-based royal commission does have the capacity to analyse things that touch on other states, provided there in a connection to South Australia."

But in a statement provided to the ABC, the commission, led by senior barrister Bret Walker SC, said it would not traverse matters already under investigation in other jurisdictions.

"The commission confirms that it will not be interfering with any current prosecutions in relation to an allegation of illegal take — to do so would be a contempt," the statement said.

"The commission will also not interfere with current civil cases, or any investigative body such as the NSW ICAC.

"It is however cooperating with, and will share information with, such investigative bodies.

"It is also pursuing matters relating to compliance and enforcement that are not involved in current court cases or investigations."

Commissioner Bret Walker is satisfied he currently has the powers to compel documents and witnesses from outside the South Australian jurisdiction. ( Four Corners )

The statement said commissioner Bret Walker is satisfied he currently has the powers to compel documents and witnesses from outside the South Australian jurisdiction.

South Australian Attorney-General Vickie Chapman told Parliament on Thursday that the new Government would not proceed with legislation to clarify the reach of the commissioner's powers.

"The Government, following discussions with Mr Walker, have determined that an amendment to the Royal Commissions Act 1917, to clarify the extraterritorial reach of the royal commission, will not be progressed."