Is govt. job prospect affected if i am charged in false criminal case?

Firstly with respect to both Government Jobs and Passport Application Form, the Candidate is required to answer the following question:

Have you ever been charged with criminal proceedings or any arrest warrant/ summon pending before a court in India?

Before answering this question, you need to understand what is the meaning of "Criminal Proceedings":

It has been held that till the time the investigations are on going i.e. before the Court has taken cognizance of the offence, it cannot be said that criminal proceedings are pending against the person. Therefore, criminal proceedings are said to have commenced once the Court takes cognizance of the offence and the charges are framed against the person.

Now if the matter has reached that stage, then you are required to state the answer as Yes and give details.

Now with respect to Government Jobs and Passports, the dependency of criminal proceedings is a criteria, however it is the discretion of the Authority to accept or reject your application. Merely because the proceedings are pending does not mean that your application shall be liable to be rejected.