Dear Rajib Paul,
If you have discovered the misappropriation of funds by the employee, then you need to order the domestic enquiry. On the strength of the enquiry report, you can lodge a police complaint. Even while lodging the police complaint also, you need to have material evidence of the defalcation. On the strength of the company's letter, the police authorities may not lodge the FIR.
Earlier, such cases have been discussed on this forum. You may refer to the following threads to educate yourself:
https://www.citehr.com/showthread.php?p=2497327#post2497327
https://www.citehr.com/621252-possibilities-legal-action-if-person-kept-under.html
https://www.citehr.com/565908-theft-abscond.html
https://www.citehr.com/639994-feedback-about-terminated-employee-mismanagement-misappropriation-new.html
Thanks,
Dinesh Divekar