This becomes a case by case basis. But, I will say that sometimes ethics complaints look like sour grapes during ongoing litigation, particularly if the proof is not absolutely compelling.
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Are you asking about an ethics complaint about your own attorney? If so, you can decide whether to hold off on this until after the case is over, so as to enable your attorney to represent you to the fullest -- or, depending on the circumstances you can fire your attorney, get a new one, and proceed with an ethics complaint at your convenience.
Generally ethical issues have nothing to do with the resolution of the case at hand, and may be a distraction. There is no statute of limitations on ethics complaints, so usually they can wait until litigation is concluded.
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If you think you have an ethics complaint against your own attorney, speak to your attorney first. It's tough to imagine an attorney continuing to represent a client who has filed an ethics charge against him. If your beef is with another attorney involved in the matter, again, speak to your attorney. What may appear to be unethical to you might not be. Secondly, if you do file an ethics charge in the midst of the matter that will look worse than sour grapes - it will look like you are trying to game the system. Good luck.
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When I served on an ethics committee for my county, we held off on investigation, and if merited, prosecution, until the underlying litigation was complete, so it could not be used in the litigation as leverage. Here is the link for more information on the process from the NJ Court's website: http://www.judiciary.state.nj.us/oae/atty_disc/atty_disc.htm
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I worked for the OAE for 20 years. Generally speaking, if there is a pending related civil or criminal case in which the facts mirror or are analogous to an ethics grievance, then the grievance will be held in abeyance. However, if the ethics grievance (the initial client gripe) has been transformed into a complaint (analogous to an indictment), OAE may still proceed. It's decided on a case by case basis. And the prevailing culture at OAE has changed from tough but fair to just plain tough. Anyone who receives a grievance should at least consult with a lawyer. Ethics cases do not proceed like a typical case. The system has its own rules and procedures. In general, the Supreme Court does not approve of using an ethics complaint as a hammer in a civil or criminal case. You can always file a motion with the Court's Disciplinary Review Board to stay an ethics case while other related matters are underway.