Company has not submitted PF for eligible employee what can be done

If company have not submitted PF for eligible employee from last 13 years. Now company ready to submit because of employee have filed complaint. What should employee get only PF amount or any other penalty amount as well according to which PF section. If company is ready to give only PF amount not any type of penalty then under which PF section they have to pay penalty amt also. PF regional commissioner have said penalty will go to PF department not to employee. Is it true ? Please confirm.