Where to complaint against dy registrar in mumbai

You must complain to his higher authority, i.e., the State Commissioner of the Societies.

Instead of adopting the route of making complaint against the deputy registrar you may file a suit for mandatory injunction against the deputy registrar before the cooperative court seeking the same relief which would be more effective 

In Delhi an order passed by a Dy. Registrar Cooperative Societies can be challanged U/S 112 or 114 of the Delhi Cooperative Societies Act, 2003 before the State Cooperative Tribunal or Financial Commissioner as applicable / provided on the subject matter.

It may slightly differ in your case / State Cooperative Societies Act, please check. 

Take help of local lawyer for proper legal guidance.