Dear friend,
When a statutory authority issues a notice for non-compliance of any statutory provision, what you have to do first is immediate compliance together with any reasonable explanation and assurance of future adherence. Then the authority may exercise his discretion to drop all further action or to proceed with any penal action.
Therefore, onlookers like us cannot guide you how to draft a suitable reply without actually going through the notice. It can be an inspection order communicating the contravention and asking for immediate compliance or a show cause notice asking to explain why penal action should not be initiated against the employer for the contravention. Even then, for certain non-compliance like failure to submit returns we cannot suggest any reply defending such contravention.