The 486-page report listed instances of payments being made to employees who had "retired, absconded, died, resigned [or] left."
Yoweri Museveni, Uganda's president, has talked tough on corruption in the country, which receives nearly half its funding from foreign donors.
But he has been criticised for what diplomats say are failures to punish wrongdoing by his closest allies and family.
In May, Jim Muhwezi, the former health minister and close ally of Museveni, was charged with stealing nearly $2m of donor cash earmarked for children's vaccines.
A few years earlier, a number of top Ugandan army officers were implicated in a "ghost soldiers" scandal in which salaries were drawn for dead or retired soldiers and then allegedly stolen.