A spokeswoman says the backlog is the result of staffing shortages within the department, which officials are trying to correct.
This is the latest in a series of grievances for reserve soldiers, who often face not only discrimination within the ranks because of their part-time status, but on an institutional level when it comes to benefits and care.
Canadian Forces ombudsman Pierre Daigle has written extensively about the treatment of reserve members, who hold civilian jobs but dedicate weekends and vacations to military training.
Daigle's office has received numerous complaints about severance and pegs the waiting time between nine and 17 months.
"The position of the ombudsman is that excessive delays in providing CF members with their hard-earned financial entitlements is unfair and potentially places a financial burden on departing member and their families," said spokesman Jamie Robertson.
The ombudsman will conduct a systemic investigation this fall, Robertson added.
Capt. Amber Bineau, a Defence Department spokeswoman, said full-time soldiers wait up to 18 weeks for their severance.
Severance for both full and part-time soldiers is based upon length of service determined by an audit of the individual's personnel file.
She said the department has received at least 13 complaints in the last year about delays getting severance cheques out.
The wait time has nothing to do with recent federal budget and strategic review cuts, Bineau added.
"The department is working diligently to fill vacant positions as quickly as possible in order to reduce this backlog and the time required to process severance payments," she wrote in a recent email statement.
"As an interim measure, temporary civilian help is being employed to assist in addressing the current issues."
Severance is calculated as seven days of pay for every year of eligible service, including partial years.
Last year, the military ombudsman chided the Conservative government over its failure to heed previous warnings about care for injured reservists, who made up a significant percentage of the soldiers deployed during the Afghan war.
Daigle documented how the government failed to implement over half of the 12 recommendations from a 2008 report and suggested part-time troops often get second-class treatment.
He pointed out that the military insurance plan, particularly dismemberment coverage, differs for reservists.
Internal defence department documents also show the military has struggled to deliver health-care to part-time soldiers who've returned from deployment.
The issue of severance pay within the military comes a year after the Harper government began an effort to clear its books of the burden of accumulated severance for federal civil servants.