Dear Subroto,
As we understood you correctly that you have centralized accounting facility in your unit but have not received the Centralized Registration from the Service Tax Department and also not provided any intimation regarding additional places of businesses but deposited the Service Tax so collected from all your branches. In our opinion since you have paid the entire service tax which was collected by you therefore, Department in worst scenario can penalize you for not obtaining the Centralized Registration Certificate. However, you can always plead for a lenient view since you have not evaded the service tax collected by you, since it is a procedural lapse at your end.
If required, we can help you out in this matter by submitting a suitable and appropriate reply to the department against impugned SCN etc.
Regards,
YAGAY and SUN
(Management, Business & Indirect Tax Consultants)