The Department for Business, Innovation and Skills (BIS) is unable to account for a quarter of its staff sickness absences.
Mental health became a more serious concern for the government organisation while the average amount of time lost per employee also grew.
According to figures released by the government department, 24.9% of sickness absences in 2014 were recorded as unknown (13%) or the symptoms were ill-defined (11.8%).
However, the figure was an improvement on 2013 when just under a third of absences (30.8%) were not properly recorded - one in five (20.9%) were unknown with one in ten (9.8%) having ill-defined symptoms.
Overall the average number of working days lost (AWDL) per employee rose to 5.6 days in 2014, up from 5.3 days in 2013.
Mental health was the biggest reason for absence, increasing to more than one in five (21.6%) in 2014, from 17.7% the previous year.
Musculoskeletal disorder fell slightly but remained as the cause of close to one in ten absences.
Sick absence data for BIS and its partner organisations also revealed the average amount of time taken off by its female employees - up to 7.2 days per year from 6.1.
In contrast, the average absence for male staff dropped from 4.5 to 4.0 AWDL.
Absences among older staff generally grew the most with those aged 50-54 increasing one full day (to 6.6 AWDL) and by 0.9 days (up to 6.8 AWDL) for the 55-59 age bracket.
The number of lost working days for staff over 65 fell by almost two days from 10.5 to 8.6 AWDL, however BIS and its agencies only employed 235 staff in this age group during the time period and so the measure could be more susceptible to fluctuations.
BIS did not answer directly when asked why it failed to fully record a quarter of its absences.
However a spokeswoman said: "Our figures are published in accordance with reporting guidelines for the civil service and average working days lost compares favourably with other similarly sized departments."
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