Independent Commission Against Corruption head Megan Latham announced on Wednesday she would not reapply for her position after her five-year term was cut short by an unprecedented Act of Parliament.

A restructured ICAC will be headed by a chief commissioner and an additional two commissioners under a plan devised by the NSW Department of Premier and Cabinet.

Ms Latham was "invited" to reapply for a position in the remodelled agency but critics have described the shakeup as a political fix to remove her from office.

Mr Cowdery said the legislation "appeared to be nothing more than a device to remove the commissioner, cloaked in some other reforms that were probably unnecessary".

"This kind of action has been taken sparingly in the past with some politically unpopular courts [or] judicial officers, but that does not make it right," Mr Cowdery said.

He said the legislation restructuring the ICAC "and affecting the position of the Commissioner was unprincipled and unwarranted".

"The Commissioner's resignation has clearly been forced by this legislated change and is entirely understandable," he said.

Ms Latham, a former prosecutor who will now return to the NSW Supreme Court bench, has presided over the ICAC at a tumultuous time in its 28-year history.

Operation Spicer, the investigation into Liberal Party fundraising before the 2011 state election, ended the political careers of a number of Premier Mike Baird's Liberal Party colleagues.

Ms Latham also saw the agency's jurisdiction effectively redefined by the High Court after a controversial failed bid to investigate deputy senior Crown Prosecutor Margaret Cunneen, SC, for which she was heavily criticised by ICAC Inspector David Levine.

Mr Cowdery said his comments had "nothing to do with the merits of any action taken by the commissioner in the past - I am concerned with the principle of independence of the commissioner, akin to judicial independence, enshrined in the legislation".

"That independence is essential to the effective exercise of the commission's powers," Mr Cowdery said.

Mr Baird said neither his legislation nor Ms Latham's resignation would prevent the ICAC from continuing or reporting on current investigations, including Operation Credo.

Operation Credo examined controversial infrastructure company Australian Water Holdings, which had links to both sides of politics and led to the resignation of then NSW premier Barry O'Farrell.

However, critics have suggested it would be practically difficult for a new chief commissioner who did not preside over the inquiry to make findings about the credibility of witnesses in a final report.