MPs have criticised "amazingly high" levels of sick leave among staff at the DVLA and the Driving Standards Agency.
Stress is a major cause of sick leave, the report found
On average, employees had three weeks a year sick leave, although that figure was bumped up by "a few people on long-term sickness," MPs said.
Public accounts committee chairman Edward Leigh said it was surprising the agencies could "function adequately".
The Department for Transport said it was improving procedures to help cut absences and address underlying causes.
The committee's report follows a critical report by the National Audit Office published in June.
The MPs' report said that overall sickness leave at the DfT and its seven agencies averaged 10.4 working days per full time employee in 2005 - which they said cost the taxpayer £24m.
While sick leave rates at the department itself and four of its agencies were below average - at the DVLA and DSA, which together employ more than 50% of all DfT staff - they were "significantly higher".
They said the DfT had only recently made tackling sick leave levels a priority, but said 75% of staff at those agencies had taken 10 days or less.
The main reasons for absence were mental health and stress, particularly among those on long-term sick leave. The Swansea-based DVLA said the most common reasons for stress were not related to work.
The report said there was a link between high levels of sick leave and relatively low-paid, repetitive, administrative jobs. It said measures had been taken to strengthen management, which was particularly important in those areas.
Mr Leigh, a Conservative MP, said: "Sick leave seems to be a way of life in two large agencies of the Department for Transport, the Driving Standards Agency and the DVLA.
"On average, each employee is off sick for nearly three weeks each year. The fact that both agencies seem to function adequately despite this amazingly high rate of absence is a matter for surprise, to say the least."
But a spokesman for the Department for Transport said: "Sickness rates in five of the eight DfT bodies are at or below the rates in comparable organisations in the public and private sectors.
"Where rates are higher we are committed to making improvements, supporting those who are genuinely sick while also addressing any underlying causes.
"We are also improving procedures to help minimise absences and allow staff to return to work as quickly as possible, for example through better management training."