He went through extensive rehabilitation therapy and was "ecstatic" when declared fit to return to working 35 hours a week, but it proved too much - he lost weight, was exhausted and permanently on the edge of depression.
His GP put him off work but the Accident Compensation Corporation refused to pay weekly compensation so he had to depend on the sickness benefit for nearly two years until, with a legal challenge pending, the corporation backed down in light of an assessment by neuro-psychologist Ralf Schnabel.
His report said in 2010 that Mr Murtagh had post-traumatic brain syndrome and permanent impairment. It recommended a maximum working week of 15 hours.
Mr Murtagh thought his troubles with ACC were over and settled into a manageable routine of part-time self-employed mechanical engineering work, up to 20 hours a week, topped up by weekly compensation.
But two months ago, ACC forced him into a new series of work-capacity assessments. He was thrown into turmoil when ACC said he could lose his weekly compensation.
"Why do I have to do [the assessments]? ... I can't believe they're allowed to put me through this. It should be illegal," Mr Murtagh said.
ACC has striven to reduce the number of long-term claimants, like him, who receive weekly compensation, achieving a cut of 25 per cent to 10,773 in the three years from June 2009.
ACC adviser Dr Evan Dryson said in a letter to the corporation that Mr Murtagh had had "appropriate rehabilitation" and the main limitation was mental fatigue. He recommended steadily increasing his self-employed hours, noting he was doing 15 to 20 hours a week, but did not state how many hours he could work.
Fitting and turning was a "medically sustainable type option", Dr Dryson wrote, adding that Mr Murtagh did not think he could do more than 20 hours a week.
ACC case manager Kristin Williams, citing Dr Dryson, told Mr Murtagh if he was found to be "substantially fit for your pre-injury work type, you will lose your entitlement to weekly compensation".
But she was uncertain if the occupational medicine specialist, despite indicating he had received all the medical information, had received the Schnabel report. She sent him a copy.
Dr Dryson's second letter said the Schnabel report made no difference to his original view of Mr Murtagh's work capacity. "Although not specifically stated by me [in the first letter], it was my opinion Warren would have difficulties sustaining work at the level of 30 or more hours per week. I remain of that opinion."
However, Dr Dryson said Mr Murtagh could cope with around 20 hours a week and suggested he would eventually reach 30.