Michael Ferguson looked at how National Defence and Veterans Affairs handled the transition to civilian life for more than 8,000 members released on medical grounds between 2006 and 2011.
The report found both departments were incoherent when communicating services, standards and expectations to the injured, and as a result many current military members and veterans did not get the expected care — or had to wait for it.
Roughly 25 per cent of medically released soldiers did not have either case management services or plans offered to them by the military.
At Veterans Affairs, about 20 per cent of veterans identified as being a risk for not successfully returning to civilian life had no case supervision.
Almost five years after the Canadian Forces ombudsman railed against National Defence for shoddy record-keeping, Ferguson's audit levelled a similar complaint, saying the department does not have a consolidated database on injured members and key information was often missing in existing files.
The auditor's report, released Tuesday, also says the poor quality of the department's data calls into question many of its benchmark health studies, such as reports last year on cancer mortality and post traumatic stress.
"According to Canadian Forces Health Services staff, the poor quality of some Canadian Forces data limits the ability to forecast the demand for services and measure effectiveness," said the audit report.
"For example, data on reservists was so poor that they had to be excluded from the May 2011 report, Canadian Forces Cancer and Mortality Study: Causes of Death."
Puts spotlight on PTSD
Ferguson's study also rapped Veterans Affairs, warning the department was not taking into account an increasing number of post-traumatic stress disorder, or PTSD, cases in the military when it forecasts for the future.
Critics levelled the same complaint last year when they pleaded for Veterans Affairs to be spared the Harper government's budget axe.
Since the beginning of the Afghan war, the defence and veterans departments have taken to delivering services jointly on military bases, something the Conservatives have cited as an example of how they've improved the system.
But the auditor says the framework "contains important gaps," and it's often unclear which department is in charge and accountable for the management of the centres.
Ferguson noted both departments have taken steps to address most of the issues, but haven't gone far enough.
National Defence and Veterans Affairs said they accepted all of the auditor's recommendations.
Care for injured members of the military costs about $500 million annually.
In a separate audit also released Tuesday, Ferguson raised the alarm about fire alarms at military bases across the country, saying that inspections were not being conducted.
There have been many infractions of the National Fire Code at installations, the auditor noted.
The study examined the management of the Defence Department's $22 billion worth of real estate and found that bases have since the 1990s done little preventive work, usually focusing their efforts on fixing things that are broken.
Ferguson says corrective action is being taken, but at some facilities the health and safety of workers could be at risk.