Tell your employer politely that as an HR person, I am maintaining the attendance log, which serves as proof of my work with you. If I go to the labor commissioner with all the necessary documents, severe action will be taken.
You can inquire whether he is paying PF and ESI to all workers. If not, that can serve as additional evidence to strengthen your case for receiving your salary.
As an HR professional, if you explain both positive and negative points to your employer regarding the potential consequences he may face from the labor commissioner if the matter escalates, you will likely receive your salary.
It may be prudent to start looking for a new job. How have you managed to stay there for 3 months? Good luck.
Regards