Darrin Bond, a former project director in the government's IT arm CorpTech, says he was against using a prime contractor for the payroll system and eventually changed departments because of it.
Bond told the Queensland Health Payroll System Commission of Inquiry in Brisbane on Tuesday that it was a private contractor, Terry Burns, employed by CorpTech, who advocated giving a prime contractor control over the system's finance, HR and payroll components.
Bond said Burns "both designed and led" the procurement process, which eventually saw Burns being appointed to a high-ranking role similar to his own.
"Certainly at the time there was a degree of resentment, but I would see it more as professional disagreement as to how the issues were going forward," he told the inquiry.
Bond said Burns had heard he raised concerns about the model with Under Treasurer Gerard Bradley.
"He ... came into my office, closed the door and was fairly aggressive in telling me I was not permitted to go and see Gerard any more," he said.
Bond said if it had been his choice, he wouldn't have gone with the prime contractor model, a fact he made clear to Bradley.
The department was too big and too complex to rush the system through, he said.
Bond said he would have at least first introduced the system into a smaller department with simpler award rates.
But after the model was decided upon and tenders were called, it was IT firm Accenture, not IBM, that was the preferred choice as prime contractor, he said.
Bond said Burns then asked the evaluation panel to reassess the selection criteria, which led to IBM being chosen.
The inquiry has already heard that Burns described himself as IBM's former "top man" in South Africa.
It also heard from former Logica general manager Michael Duke, whose company also bid for the contract.
Duke said his tender failed because Logica bid for only part of the contract, feeling it would not be possible to complete what the government required, especially within the budget.
Health minister Lawrence Springborg has estimated the failed payroll system will cost taxpayers $1.2 billion.
Thousands of public servants were underpaid, overpaid or unpaid after IBM's flawed computer system was introduced in March 2010 by the then Labor government. More than 50,000 staff are believed to have been overpaid more than $90 million.
The inquiry before Commissioner Richard Chesterman will continue on Wednesday.