Deputy Attorney General Richard Fyfe received complaints from employees of the IIO, and asked the Public Service Agency to investigate, said a statement from the Ministry of Justice.
Fyfe asked the agency "to conduct a fair and thorough investigation in order to ensure personnel practices in the IIO are in accordance with the law," said the statement.
The IIO was created in 2012 with a mandate to review cases in which people are killed or seriously injured by police officers.
It is headed up by a chief civilian director, who has never been a police officer, and has 50 employees.
Individual investigators must be five years removed from police work before joining.
The Ministry of Justice won't comment on any firings, wrongful dismissal suits or severance packages.