Plant and machinery on lease

The terms are not clear: you have taken plant and machinery on lease or the business of the firm? 

Unless you rectify the basic fault, nothing can get solved, unless of course, the mentality of the owner gets changed.

Plant & machinery and lease to run the business in the scheduled property for 3 years

You should obtain factory license in your name, and thus open current account being you as new proprietor, so that the amount gets deposited in your account.

I have obtained factory licence in my name and currently running business in my name only. But one licence which is mandatorily required to run the factory is still in his name. Now, owner is going to that govt. dept. (which is responsible for issuing that licence) and making complaints against me. 

Formost thing to sort out is your relation with the owner, so that any more complication may not arise in future, and the financial issue can get settled.

As far as future payments are concern, based on your registration with any governmental agency and lease agreement, you can open a current account with any bank, and get cheques deposited in your own acc.