Transport Minister Stirling Hinchliffe has resigned in response to a damning commission of inquiry into a driver shortage and timetable failures at Queensland Rail.

Deputy Premier Jackie Trad will become acting minister in his place.

Consultant Phillip Strachan's commission of inquiry, released today, found complacency, a reluctance to share bad news and an "unwieldy" management structure led to last year's rail service disruptions in south-east Queensland.

Premier Annastacia Palaszczuk said she had accepted Mr Hinchliffe's resignation, but also offered her thanks to Mr Hinchliffe for his work "to manage the very challenging issues at Queensland Rail".

Ms Palaszczuk also revealed she had appointed Mr Strachan as the new QR chairman.

Mr Strachan's report makes 36 recommendations, including a drastic overhaul of the Queensland Rail executive.

The inquiry was instigated in response to a shortage of drivers, timetable problems and service cancellations that emerged after the Redcliffe Peninsula line opened last October.

It recommends stripping out up to three layers of bureaucracy from the chief executive to frontline workers in a bid to improve information flows and highlight potential problems earlier.

'No minister could have foreseen the driver shortage'

Mr Hinchliffe issued a statement saying while his resignation was a tough personal decision, he believed it was in the Government's best interests.

"The issues at Queensland Rail have been some of the most challenging and, at times, frustrating issues I have needed to manage as a Minister," Mr Hinchliffe said.

"I know that they have been a distraction for the Government's core task of delivering jobs for Queenslanders.

"The findings of Mr Strachan demonstrate that no minister or government could have foreseen [the] driver shortage issue due [to] Queensland Rail mismanagement.

"I'm pleased that following a rough slog we have been able to begin to turn this issue around and today marks a line in the sand on the matter.

"At the Premier's request I shall remain Leader of the House and will be recontesting the next election to continue as the Member for Sandgate."

'A management culture relying on intuition'

Mr Strachan found the issues that caused the problems have compounded and grown over recent years, including a significant increase in the need for new crews between 2014 and 2016, when the supply of qualified drivers declined by 4 per cent.

Annastacia Palaszczuk appointed Phillip Strachan as QR chairman. ( ABC News: Chris O'Brien )

He found the driver shortfall was not widely understood across QR, which had a culture of "relying on intuition, complacency and being reluctant to share bad news".

He said QR's chief executive did not actively investigate whether adequate measures were being taken to address the crew shortage, and the QR board was not informed, so did not report the problem to the State Government or the public.

Mr Strachan described QR's structure as unwieldy, with eight layers of bureaucracy resulting in "complex and ineffective governance".

His inquiry outlines a range of fixes to boost train driver numbers, including opening recruitment to external applicants, including those with no previous rail experience.

The report recommends QR "deliver and maintain a structural surplus of train crew" to avoid a "systemic reliance" on overtime.

It said QR management should also exercise discretion over granting leave and recommended the chief's executives responsibilities be extended to include formal approval of timetable changes.

The inquiry found that despite working hard to recover from the crisis, QR only expected to resume regularly timetabled services by late next year.