A parliamentary inquiry into the body resumed on Thursday, with Treasury secretary Paul Grimes being questioned a day after a "scathing" report from the auditor-general.
Auditor-General Margaret Crawford will also appear at the inquiry on Thursday after delivering the audit of the state's finances and TAHE, the state-owned corporation with assets including trains, land, rail equipment and infrastructure.
Dr Grimes called for a new, independent investigation into the conduct at TAHE, despite the auditor-general's report finding the department was too reliant on external consultants.
"I believe it's appropriate to initiate an independent assessment within the department," he told the public accountability committee.
Ms Crawford's findings "warrant serious investigation" by an "independent assessor", but what the report found was confined to "processes" and further conclusions would need to be referred to a new, independent review, Dr Grimes said.
The auditor-general criticised Treasury's "undue reliance" on external consultants, creating risk that "agencies shop for opinions from multiple experts in order to receive advice that matches the outcome being sought".
TAHE Chair Bruce Morgan said the report was a milestone for the corporation, pointing out the auditor-general had marked the corporation's financial reporting as fair, despite her concerns.
"I don't find (the issues raised) that unusual for a start-up organisation," Mr Morgan said.
There was no indication from the auditor-general TAHE was at risk of not having its audit signed during the draft stage, he said.
TAHE CEO Benedicte Colin would not be drawn on who was responsible for handing "late, unsophisticated, and inaccurate forecasts" to the auditor-general.
Ms Colin said the company, currently facing a $20 billion loss, had a "number of levers" to increase revenue including access and licensing fees over its assets.
NSW Transport secretary Rob Sharp said the process of moving assets from RailCorp to TAHE had been "challenging".
In December Mr Sharp signed an agreement pledging $5.2 billion in access and licence fees to TAHE over the coming years.
He said the price was recommended by the Independent Pricing and Regulatory Tribunal.
On claims Treasury had been "obstructive and difficult" and released thousands of pages of documents hours before the auditor-general was due to sign her report, Treasury chief financial and operations officer Stewart Walters said documents were requested late.
Ms Crawford's report on the state's finances followed her delay in signing off on the accounts due to "significant uncertainties about TAHE".
The opposition and Greens have labelled its findings "scathing".
Premier Dominic Perrottet said auditor-general reports were generally critical of government.
"I absolutely stand by (TAHE)," the premier said on Thursday.
"It is the right approach in terms of the management of state transport assets.
"It's not something that the NSW Treasury dreamed up. It's something that has been led in other jurisdictions."
If there were issues between Treasury and NSW Transport that had led to engaging with the auditor-general, "then we will take that on board and improve those processes", he said
Opposition treasury spokesman Daniel Mookhey called on the premier to sack TAHE's board, saying the corporation had "burned a huge hole in NSW's finances".
"TAHE looms as the worst financial disaster to hit NSW in living memory."
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