The Northern Ireland office lost an average of 10.3 working days per person in 2012, almost ten times the number lost in the Scottish Office, government statistics show.
However, performance improved from 2011, when 12.1 days were lost.
Other departments with high absence rates included the Ministry of Justice (8.9 working days lost per person) the Ministry of Defence (8.1) and the Home Office (6.9).
The lowest number of working days lost was recorded by the Scottish Office (1.7) followed by the Cabinet Office and Energy and Climate Change.
The figures, which were released in response to questions by the Conservative MP David Ruffley, indicate that government departments have struggled to manage absence.
Over 60% of departments recorded rates in excess of last year's UK average of 4.5 days lost per worker.
And while the majority of departments recorded a decline in the number of working days lost since 2011, rates for five departments rose.
A Northern Ireland Office spokeswoman said that the figures stated for the department were due to a very small number of long-term sick cases.
"If the three staff on long term sick leave are excluded, then figures for the Northern Ireland Office would be 1.4 % in 2010-11 and 1.9 % in 2011-12 respectively," she said.
"All absences are dealt with through internal managing attendance process and procedures.
"Those members of staff to whom the long term absence relates no longer work in the NIO."
Lowest number of working days lost:
Scottish Office 1.7; Cabinet Office 2.5; Energy and Climate Change 3.6
Highest number of working days lost:
Northern Ireland Office 10.3; Justice 8.9; Defence 8.1