You did not mention details about your employment and the year of retirement. Generally, every civil service rule has a limitation period for prosecution of the retired employee. If there is a delay of more than four years, you are entitled to prefer a petition before the appropriate Court or Tribunal for quashing of the preceding. The Supreme Court has stated in several judgements that the launch of prosecution after an inordinate delay is unlawful.
According to article 21 of the Constitution of India, every person has the right to get speedy justice. The prosecution is illegal if the government keeps the investigation pending or sanctions the inquiry after a long time of retirement. Generally, the court does quash the proceeding if it is launched after more then four years.
In State of Punjab v. Kailash Nath, (1989) 1 SCC 321 the supreme court held that departmental enquiry after four years of retirement is pervasive and liable to be quashed. If the employee is guilty of any offence punishable under the Indian penal code or the prevention of corruption act, then the above said limitation period would not apply.
Hence, if no criminal liability arising from the act committed during the service, then and the department cannot prosecute the employee. If that act constitutes criminal liability, then the department and the government have the liberty to prosecute. However, it is not clear whether any criminal liability accrued out of that negligence.
If not, then the prosecution is unlawful and you have the right to challenge it before proper forum. You can file a petition before the Central Administrative Tribunal if you are a Central Government employee. However, you can also move a petition before the high court under article 226 of the constitution of India.