Under section- 156(3) of Cr.P.C.

2006(3) Criminal Court Cases 820 (Bombay)

The above case says that magistrate has powers to deal issues even if the matter is civil in nature.

Apex Court has time and again drawn attention to the growing tendency of complainants attempting to give the cloak of a criminal offence to matters which are essentially and purely civil in nature, obviously either to apply pressure on the accused, or out of enmity towards the accused, or to subject the accused to harassment. Criminal courts should ensure that proceedings before it are not used for settling scores or to pressurise parties to settle civil disputes. But at the same, it should be noted that several disputes of a civil nature may also contain the ingredients of criminal offences and if so, will have to be tried as criminal offences, even if they also amount to civil disputes. See: G. Sagar Suri v. State of U.P. 2000 (2) SCC 636 and Indian Oil Corporation v. NEPC India 2006 (6) SCC 736.

 Surprising that a civil case has been taken up by criminal court.

 Anish have suggested the best remedy.

i would suggest wait till the summons are issued to you, the matter has been directed for investigation, and you have yet not been summoned at this stage.

the police may give report in your favour and the court may accept it.

It is not uncommon to see matters of civil nature reaches Police station through magistrate court u/s 156(3) CrPC.

Police will give a final report to drop further action citing that complaint is of civil nature.

It is better to wait till the final report is filed before the court. I suggest to follow the advice given by Kiran Kumar.