Termination of employee - can labour officer send notice to school?

We Are having an clerk in our school. he had done theft in our fee and not deposited the same in bank account. He also given us the acceptation letter that he had done the theft in account. now he had done complain in labour law to re joining at our school. Kindly advice that can labour officer send notice to school or education dept will do the same.

The notice sent by Labour Officer is not invalid. You need to defend yourself properly, so pl consult a Labour Law professional and act accordingly.

What is the content of the letter from Labour officer?
Most probably the complainant may not have told the full truth to Labour officer.
Collate all evidence about theft-when, how much, how it was found and related documents like Deposit slip, passbook, fee collection record and also his acceptance of guilt letter.
The locus standi of labour officer arises when complaint is received from organisations in his jurisdiction.
Keep a proper reply ready, vetted and cross checked by Local lawyer and reply as directed in the notice.

Dear Bansi parmar,
There is no mention whether your School is a Govt-aided private school or otherwise.
Whatever it be, your school is an "industry" and the clerk employed therein is a " workman " under the provisions of the Industrial Disputes Act,1947. As such, if any complaint regarding the employment or non-employment of any such workman is received, the Labor Officer is bound to make an enquiry into it, conduct conciliation proceedings and bring about a settlement of the dispute or issue a certificate of failure of conciliation to the Government. In case of dismissal, the workman can directly go to the Labor Court on receipt of the certificate.
There is also no mention in your post whether you terminated him orally or in writing. You ought to have issued a charge-memo to him, obtained his reply in writing, if he has admitted the charge unconditionally, you can terminate his services by a formal orders in writing; If not you should have conducted a domestic enquiry giving him all reasonable opportunities and based upon the findings of the enquiry officer, terminated him.

The posted material is insufficient to advice anything good. You need to contact a lawer deals in labour cases with all documents pertaining to case.