Dear Raj,
You have to check with your Payroll office first about the discrepancy. You can withdraw EPS amount only when you are withdrawing EPF amount, and that too if you have not completed ten years of service. If you have completed ten years of service, then there is no way to withdraw your EPS amount. You will receive a Pension Scheme certificate for the EPS amount.
You can withdraw the contributed EPS amount along with your EPF balance. But the condition is you must not have completed 10 years of service. When you withdraw EPF, you will receive EMPLOYEE + EMPLOYER EPF contributions + Interest earned on this EPF. Along with that, some percentage of EPS contribution will also be paid.
You'll find some more details about the EPS from the attachment.