A commission of inquiry has been told the tender process for Queensland's failed health payroll system was unusual and may have been extended to give IBM an advantage.

The Queensland Health Payroll System Commission of Inquiry, sitting in Brisbane, is investigating how the former state government's attempt to upgrade its health payroll system went so badly wrong, costing taxpayers $1.2 billion and incorrectly paying health staff.

It is also looking at how and why IBM won the tender for the work.

IBM beat competing company Accenture for the bid, despite scoring lower on initial evaluations.

Marcus Salouk from Accenture told the inquiry that while his company's bid was more expensive, some items in the IBM bid were not costed.

He said it appeared some of Accenture's bid information was used by the Labor state government to give IBM an advantage.

But Mr Salouk said he could not provide definite proof that this occurred.

The inquiry is due to sit for two weeks and hear from 23 witnesses.