My job is to conduct investigations and report on their results to the minister's office. I have never had to make such a decision, but I think that, if the situation presented itself, this decision would be made when the investigation's results were reported.
Investigations are carried out independently. They are finalized, and their results are reported. The chain of command does not get involved in the investigation process. The chain of command is informed on the investigation's conclusions after the report has been presented to the minister's office. It would probably be at that point that the chain of command would share its concerns with the minister, who would then make the final decision.