The resignation letter from David Chandler has already been sent to the state's anti-corruption body, and was made public on Thursday.
"My personal experience has been one where engagement with the minister (Eleni Petinos') office has been problematic," Mr Chandler wrote in his resignation letter on July 7.
"A similar experience has been reported to me by other officers in the department and important pieces of previously canvassed legislation have now run into serious disruption."
Mr Chandler was hired to clean up the state's building industry after a series of defects were found, including at the Sydney residential buildings Mascot Towers and Opal Tower.
When he was brought on as building commissioner, he was confronted by "frankly horrific" circumstances in the residential apartment industry.
Mr Chandler said his disintegrating relationship with Ms Petinos was impacting confidence and momentum of the reforms in the industry.
He said after considering all the issues he faced, his role became unviable.
Mr Chandler raised concerns about the relationship between Ms Petinos and Coronation Property Group, at a time when Mr Barilaro was serving as the property group's executive director.
"These concerns crystallised at the time of the Stop Work Orders issued under the Design and Building Practitioner's Act, Declared Design Audit," Mr Chandler wrote.
The stop work orders for the western Sydney construction site were issued in April.
"I received a call from the minister's office shortly after a draft order was issued on Coronation's Merrylands development," Mr Chandler wrote.
"Shortly after that call, a message was sent to me by John Barilaro who I was advised had recently joined the Coronation Board.
"This contact came to me as a message on my personal phone requesting a meeting with me."
Mr Chandler said he copied the message and sent it on to Secretary of the Department of Customer Relations Emma Hogan.
He later met with Mr Barilaro to answer his questions.
In June, Ms Petinos asked Ms Hogan to investigate Mr Chandler over allegations he had advised banks not to work with certain certifiers, and had misled the parliament when asked about it.
Mr Chandler was later cleared of the allegations, although he resigned from his role in the same month.
"After 50 years in this industry, my character and ethical standing has been beyond reproach," Mr Chandler said.
His role had recently been extended through to mid 2023, and he said he believed this was due to his good performance, and he was supported by the industry "unreservedly".
"The challenges that confronted the NSW residential apartment industry at the time of my appointment where frankly horrific and highly politically charged," he said.
Premier Dominic Perrottet told parliament Mr Chandler's letter had been referred to the ICAC "out of an abundance of caution".
The letter was sent to the ICAC on August 1, one day after Ms Petinos was sacked as a minister amid bullying allegations.
The premier said he become aware the letter had been sent to the ICAC on Tuesday night.
Mr Perrottet insisted Ms Petinos' sacking was not linked to Mr Chandler's resignation.
Mr Barilaro worked as the executive director at Coronation Property from February to May.
