If there is a specific reason that you don't trust the HR person, then it's important to speak up immediately. For example, if the HR representative and your supervisor are personal friends if you complained to the HR rep but they did nothing about the complaint, if the HR rep violated your confidentiality by sharing the complaint with a person without the need to know, etc. However, if your reluctance stems from just a general distrust or discomfort with nothing specific to back it up, you may be hard-pressed to alter the way they do their investigation. You can still try by. Ask to talk privately with the investigator about the investigation process and surface your concerns.