The commissioner presiding over one of the biggest-ever NSW corruption inquiries has refused to disqualify himself from hearings focused on ex-mining minister Ian Macdonald.

The Independent Commission Against Corruption (ICAC) is probing a coal exploration licence granted by Mr Macdonald in 2008 to a group of entrepreneurs, including former union boss John Maitland, in its Operation Acacia hearings.

Acacia follows the long-running Operation Jasper, in which ICAC investigated another licence granted by Mr Macdonald, from which his one-time colleague Eddie Obeid allegedly made millions.

Commissioner David Ipp, QC, has overseen both operations and is yet to deliver findings.

On Thursday, Mr Macdonald's counsel Tim Hale called for Mr Ipp to remove himself "from further investigation in both Operation Acacia and Operation Jasper on the grounds of apprehended bias".

Mr Hale said evidence aired in the Supreme Court last week showed Mr Ipp could be seen to be not acting impartially in the ongoing proceedings.

Written submissions tendered to the court on behalf of mining magnate Travers Duncan on Friday showed that in the midst of Operation Jasper, Mr Ipp met with the Department of Premier and Cabinet to discuss the development application for an open-cut mine at Mount Penny.

Shortly afterwards, the commissioner sent advice to the department's director-general, Chris Eccles, saying the minister could declare the Mount Penny mining project a "state significant development," thus allowing the matters before ICAC to be taken into consideration when determining its approval.

But Bret Walker, SC, for the attorney-general, said Commissioner Ipp had done nothing to show apprehended bias, as there was "no hint" that he had advised the government to refuse the application.

On Thursday, Mr Ipp confirmed that he had no intention of standing aside.

"I understand the application, I understand why you make it," he said.

"My reasons for declining it are the same as those advanced by Mr Walker in the Supreme Court."

The commission is now hearing from Ian Murray, CFMEU general vice-president for mining and energy, who has told the inquiry he was close to the union's retired boss Mr Maitland.