Instead the commission president, a former state magistrate and coroner, ended up apologising to the inquiry after going on a rant about a crude drawing of male genitals on a document, saying the artist should have ''his head removed from his body''.

The incident will raise more questions about the Defence Department's Commission of Inquiries, which has been criticised in the past for failing to uncover the truth and being overly concerned about the reputation of the department.

The inquiry was established last year to investigate how Sapper Jordan Penpraze, 22, died when the truck in which he was a passenger rolled at Holsworthy, in south-west Sydney, in 2012.

Fairfax Media has learned that the inquiry has focused on the conduct of the truck driver, Sapper Alexander Gall, with evidence emerging that the then 20-year-old had been allowed to operate the large Unimog vehicle despite having received only 32 hours of army driving experience and having only held a learner's permit in civilian life.

The inquiry was suspended late last year after NSW Police charged Sapper Gall with dangerous driving occasioning death and six counts of dangerous driving.

Sapper Gall, who it is understood denies the charges, has since appeared in Downing Centre Local Court and been remanded on bail to reappear later this year.

However, before the inquiry was suspended, an extraordinary exchange took place on day 24 of its hearings last year, which led to an admission from the president, Group Captain Warren Cook.

''I've made some very stupid and very uncalled-for remarks earlier this morning. Please accept my deepest apology. It was stupid and I've had my piece of stupidity for the day and hopefully for the week and the month,'' he said.

Captain Cook appeared to be referring to his conduct earlier in the day, when he spoke out after hearing evidence in relation to Sapper Gall's training.

After seeing an exam paper relating to the driver training, Captain Cook raised a question about Sapper Gall's name written on the paper, which appeared to have been annotated with a crude drawing of testicles.

''I'll simply say this, and I'll say it as neutrally as I can: if I look at the way that gentleman's written his name, if that had been handed to me, there'd be some suggestion about his head being removed from his body,'' Captain Cook told the inquiry.

Later, asked about the relevance to the terms of the inquiry, Captain Cook said: ''At the risk of sounding very … no, I'll withdraw that.''

The inquiry had earlier heard significant evidence of training standards for army drivers being well below that required for civilian drivers of buses carrying the same number of passengers.

It heard that the accident occurred only five days after Sapper Gall had completed the army's driver training course, which had involved him gaining a total of 32 hours' driving experience, only 14 of which were on driving trucks.

Asked this week if driver training standards had changed, an ADF spokesman said that following the crash, Defence had ''reviewed and updated road transport policy, procedures for general military driving and risk management processes''.

''These changes include the carriage of personnel in appropriate seating and reinforcing safety for all driving tasks,'' he said.