The state-owned Queensland Rail (QR) has been plunged into chaos in recent weeks.

Driver shortages, service cancellations and executive re-jigs have led QR’s new acting chief executive to describe the situation in the following terms;

“I don't think it's a shemozzle ... I don't think it's our finest hour.”

The problems started after the opening of the Redcliffe Peninsula Line in early October, which was meant to be combined with an increased frequency of services.

It triggered what QR said was an unforeseen driver shortage of four drivers and three guards, which have since led to over a hundred services being cancelled.

Former QR chairman Michael Klug and former CEO Helen Gluer resigned last week after admitting that the planning for the new line was seriously flawed.

Neil Scales, director-general of the transport department, was then appointed as QR's interim chief executive.

The focus has now turned to what State Transport Minister Stirling Hinchliffe knew about the situation, and when.

Mr Hinchcliffe says he was not given a copy of a report prepared by external consultants for Queensland Rail in January this year, which warned of the impending train driver shortage.

He later Hinchliffe admitted that public transport advocate Paul Pluta had emailed him in March to warn of driver shortages linked to a new fleet of trains, but still claims only learned about the January report from journalists this week.

Mr Hinchliffe has resisted calls to step down, and narrowly escaped a no-confidence motion in Parliament on Tuesday.

He is now on to a related issue, asking QR's finance department to find out exactly how much each of the several recent timetable changes have cost.

Report has suggested the cost is about $30,000 for each timetable alteration, but Mr Hinchcliffe says that is not the issue.

"If these reports were costing a $100 and they were ignored, then I'm furious, I'm outraged, and it demonstrates a gross mismanagement of Queensland Rail,” Mr Hinchliffe said.

“It's something that the commuters on the south-east Queensland rail network should equally be outraged about.

“If a report is commissioned for a purpose, the purpose is usually to act upon it, not to pretend it was not there, and that's what myself and a lot of commuters think has happened.”

Premier Annastacia Palaszczuk has ordered an independent inquiry into the transport minister’s claims that QR misled him.