Dear Vishwas,
The stamp paper agreement is not valid as per law, as ESI & PF are the statutory benefits to the employees, if the establishment covers under ESI ACT & EPF Act. Check the applicability to your establishment by referring the acts.
If Employee Gross Salary is <15000/- , he should be covered under ESI and Basic Salary < 15,000/- he should be covered under PF and the deductions should be done accordingly irrespective of your stamp paper agreement, otherwise Employer will be penalised by the concerned authorities.
Thanks&Regards
Prathap
Senior Executive-HR
Narayana Health