The simple answer is rarely. Unfortunately, where an employer includes language in its employee handbook that the handbook is not intended to be a contract, that its employees are employed “at will,” and/or that the terms can be enforced at the employer’s discretion, the promise in the handbook that employees will be free from retaliation for reporting misconduct are ephemeral. (Please understand this is different from retaliation for reporting discrimination in the workplace or under a specific whistleblower statute. Under those circumstances the legislature has made it the law that you are protected from retaliation for making a good faith reporting.)
Employees should be cautious in their dealings with Human Resources, and wary of any promises, whether written or oral, that they will be protected from retaliation for reporting any misconduct directed towards them or others. Employees who feel they have no choice but to report misconduct, should do so in writing following confirmation from HR that they will not be retaliated against for doing so per the employee handbook.