I have replied to some similar questions earlier, which may be relevant to your question as well. Please see:
Legally speaking, there is no prohibition for conducting departmental enquiry when criminal case on the same charge is still pending in the court. It is in the discretion of the competent authority.
As I have mentioned in answer to another question, sometimes, even though the charge in the departmental enquiry as well as in the criminal case may be the same, they may have to be looked at from different angles; for example, the charge in a criminal case is based purely on the legal definition of the offence, whereas the charge in the departmental enquiry may involve the ethical or moral questions also. A departmental misconduct has a much wider scope than an offence. But, it all depends on the facts of an individual case.
Having said that, it is possible for you to challenge the penalty imposed on you in the departmental enquiry on the merits of the case, and more so, if it depends on the outcome of the criminal case pending in the court.
Dr. Ashok Dhamija is a New Delhi based Supreme Court Advocate and author of law books. Read more about him by clicking here. List of his Forum Replies. List of his other articles. List of his Quora Answers. List of his YouTube Videos.