It sounds like your employer conducted an insufficient investigation if, in fact, the witness identified by the employer supports your version of events. I would try to rectify the problem by getting a statement from the witness to give to the investigator. If you are being "railroaded", you may have a claim if the motive for the retaliation is based at least in part on some protected characteristic (e.g., race, color, creed, etc.) or some protected activity (e.g., whistleblowing, complaining about discrimination/harassment/retaliation, taking approved medical leave, etc.)
The conduct you report is not unlawful unless the motivation for the accusation is based on your membership in a protected class of people, or because you engaged in legally-protected conduct. Your facts do not disclose any such motivation.
Employers are allowed to be unreasonable, irrational and rude. They can have employees who treat other employees without respect, or who make it difficult on others based on favoritism, nepotism or down-right bad attitudes, as long as the motivation is not unlawful.
That said many corporations have internal rules that are more protective than the law where the goal is fostering a healthy and productive work environment. If you work for such a company, it makes great sense to report this directly to the Human Resources department.
Good luck to you.
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Responders here are assuming that US or California law applies to these facts. That may not be the case. If I recall correctly, what matters is what flag your ship is commissioned under, the jurisdictional rules and regs of your ship company, and where the ship was when the alleged misconduct occurred. If you are represented by a union or association of employees, you will instead have the rights that your union has bargained for.
I am flagging your post to receive the attention of maritime and admiralty law attorneys.
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You certainly have an employment law issue. Based on the fact that you were out to sea, to cover all bases you need to consult with a maritime law lawyer. There are many different peculiar rules that regulate many activities on ships.
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I concur with Ms. McCall in that there is not sufficient information to give you a meaningful response. There are really two questions involved. First relates to your chain of command. If the bosun and mate are making unfair allegations your only real remedy is to go to the master if you want to stay on that ship (or likely with that company). You had better have all your ducks in a row and facts ready to present if you jump the chain of command and take something direct to the master of the vessel, so put some serious thought into it before you just plunge ahead.
With respect to your legal rights: The first consideration is the flag and home port of the vessel you serve on. That will provide the governing law on how far the employer can push you. Note that the employer will be allowed to push you, the question really boils down to how far they can push you.
Second, you will receive the benefits of any union or merchant marine association recognized by that jurisdiction. The union representative or cob will be the person to talk to about what protections are afforded by the association, contract, union or the like.
That is pretty much all the advice I can give without a whole lot more information about the unique facts of your case. If you are serving on a US flagged vessel operated by the merchant marine, your union contract will have specific and detailed protections for all sorts of conditions well past the protections of the law.
Under U.S. law -- which may not apply at all to your situation -- the primary remedy for constructive termination is pay earned to date and one month's pay as damages. See 46 USC § 10313(c).
I would strongly suggest that you seek the advice of an attorney the next time you have any substantial liberty time away from the ship. It sounds from your question that you are a native English speaker, if the master is not a native English speaker, try to find an attorney who is fluent in both languages. If the attorney has to make any contact with the vessel or the company running the ship, the master will be the primary gatekeeper of information in any event.