Deputy Opposition Leader Tim Mander says the resignation of Queensland Rail's chairman is a sign Labor's "rail fail" is here to stay, after Phillip Strachan announced he would be leaving the job yesterday amid the executive bonus furore.

The ABC understands Queensland Rail (QR) directors Paul Wallis and Sandra Birkensleigh have also resigned.

"There is no end in sight to this mess," Mr Mander said.

"If the Premier was serious about ministerial accountability, she should act and sack Transport Minister Mark Bailey immediately."

The State Government appointed Mr Strachan as QR chairman in February last year on the back of his "comprehensive review" of problems with train crewing practices.

Earlier this week it was revealed the QR board had approved $3.6 million of bonuses for senior management, despite ongoing issues with the rail network.

The Queensland Government was forced to intervene to block bonuses of up to 15 per cent, which would have been given to about 380 senior staffers.

Speaking on Wednesday, Transport Minister Mark Bailey called the board's decision a "serious error of judgment".

"I was furious and I think commuters would be furious as well, so I made the point very clear, so that's why a directive was issued at the earliest possible time by myself and the Deputy Premier to stop this occurring and it won't go ahead," Mr Bailey said.

Stirling Hinchliffe quit as transport minister in the wake of the QR inquiry. ( ABC News: Patrick Williams )

However, Mr Mander said the Minister had earlier signed off on the bonuses.

"There are clearly fundamental problems at Queensland Rail and Minister Bailey has proved incapable of managing his portfolio," Mr Mander said.

"The buck stops with Mark Bailey — the $3.5 million in bonuses for executives were in the annual report that the Minister and Treasurer Jackie Trad signed off on, and it's time for him to go."

Premier Annastacia Palaszczuk appointed Mr Strachan to the QR chairman's job on the same day his inquiry's findings were publicly revealed.

"Phillip Strachan is uniquely placed to lead the organisation through what will be a significant transition to focus on its customers — the travelling public," the Premier said at the time.

The Rail Tram and Bus Union (RTBU) said in a statement that QR needed more people in the decision-making bodies with industry knowledge.

"We consider that decisions of the board have contributed towards the recruitment problems within Queensland Rail," the statement said.

"We have every confidence that the Queensland Government will take into accounts the needs of the industry when determining the replacement of Mr Strachan."

Mr Strachan was brought in to conduct a commission of inquiry in 2016 after hundreds of train services were cancelled because of a shortage of train drivers and guards.

His investigation found there were systemic issues with recruitment, and that QR had a culture of "complacency".

Stirling Hinchliffe was forced to resign as transport minister in the wake of Mr Strachan's damning findings.

Mr Strachan's resignation prompted the Opposition to call for the current Minister to follow suit.

'I have witnessed a major transformation'

QR timetables have been operating on reduced services but the organisation has promised to return to a full contingent by the end of 2018.

Last Friday that benchmark had not been reached when the board approved the multi-million-dollar bonuses.

In a letter to staff informing them of his resignation, Mr Strachan said he was proud of the work his team had delivered over the past 19 months.

"As a team we have maintained a constant and strong focus on implementing the recommendations of the 2017 commission of inquiry and successfully stabilised our services," he said.

"I have supported and witnessed a major transformation in the culture and performance of the organisation and am pleased to have been part of it."