The findings are likely to be used as ammunition by public sector unions in their battle with the Treasury Board over proposed changes to government sick-leave policies.
The report shows wide variances in the amount of sick leave taken from one department to another.
But parliamentary budget officer Jean-Denis Frechette says most departments don't have policies in place to backfill for sick leave.
"Since most departments do not call in replacements when an employee takes a sick day, there are no incremental costs," said the report released Wednesday.
Exceptions to that finding include departments where absences have a direct impact on service levels, health and safety.
Correctional Service Canada, for example, is required to maintain minimum staffing levels for the protection of the public, staff and inmates at federal prisons.
But in most cases, the report said, federal employees who call in sick are not replaced, resulting in no additional cost to taxpayers over and above regular public servant salaries.
Collective bargaining is currently underway between Treasury Board and 17 federal unions, with the government pushing for restructuring of benefits to reduce costs.
The governing Conservatives hope to cut the cost of public service pension, disability and sick leave benefits as part of efforts to balance the federal budget by next year.
Treasury Board President Tony Clement has said sick-leave costs are unsustainable and that the system needs to be revamped. The unions have complained that Clement used inflated figures to justify proposed cuts.
Public servants are allowed 15 days of paid annual sick leave. And, on average, they take 11.5 days off due to illness, says the PBO.
But unlike most private-sector firms, where annual sick leave is granted on a 'use-it-or-lose-it', basis, federal workers can carry over their annual allotment from year to year.
In some cases that has resulted in civil servants being owed several days or weeks of paid time when they leave their jobs.
The report found that sick leave can range from a low of 0.16 per cent of total departmental spending to 2.74 per cent on the other end of the scale.
The numbers are based on expenditures in the 2011-12 fiscal year.
The report also found that, in most cases, paid sick leave is proportional to departmental spending on regular wages.
"In other words, the more a department spends on wages, the more it spends on sick leave," the report said.
In February the office published a report that estimated time lost due to illness in the federal civil service amounted to the equivalent of $871 million in regular wages in the 2011-12 period.
The latest report was compiled after a request from New Democrat MP Paul Dewar and looked at data from 20 departments.
It found that Correctional Service Canada, Human Resources and Skills Development Canada and the Canada Border Services Agency consistently reported the highest average number of paid sick days per employee.
All three departments have minimum staffing level requirements to maintain operations.
In some cases, however, data was either incomplete or departments failed to provide numbers, said the report.
The border agency also noted that it does not track the cost of filling positions left vacant due to employee illness.