The Commissionerate is under the jurisdictional control of Chief Commissioner, Customs, Central Excise & Service Tax, North Eastern Region, Shillong with the following hierarchy.

     Commissioner                          --- Head of Department

     Additional/Joint Commissioner     --- Administrative Head of Divisions

     Deputy/Assistant Commissioner  --- Head of Divisions

     Superintendent                       --- Range Officer

     Inspector                               --- Sector Officer

The jurisdiction of the Commissionerate has been divided into five Divisions. The service tax work of the Commissionerate has been assigned to one division only. The area of a Division depends upon the density of the industry, service providers and complexities of the commodities & services being dealt by the Division and quantum of revenue receipts. Each Division is headed by a Deputy Commissioner/Assistant Commissioner and assisted by Superintendents and Inspectors in the Divisional office besides the ministerial staff and an Administrative Officer.

The jurisdictional area of a Division is again divided into Ranges. The jurisdiction of a range is also governed by various factors, which govern the area of jurisdiction of a Division. Each range is headed by a Superintendent designated as 'Range Officer'. Each Range Officer has Inspectors in his charge. Each inspector is in-charge of certain number of units, which varies from Range to Range. The jurisdiction of an inspector is called 'Sector'.

Each division is placed under the supervisory control of an Additional Commissioner/Joint Commissioner.

Additional/Joint Commissioner (P&V) is in charge of personnel and vigilance matters. Additional/Joint Commissioner (Review) is responsible for review of adjudication orders passed by various original and appellate authorities and for filing of further appeals against the orders which are not legal and proper.

The primary function of a Customs, Central Excise & Service Tax Commissionerate is to implement the Customs, Central Excise & service Tax Acts and the Rules framed under various provisions of these Acts, Central Excise Tariff Act / Customs Tariff Act and other allied Acts of the Parliament of India under which duty of Central Excise or other such duties/tax which are levied and collected in the manner in which Central Excise duty is levied and collected. For discharging the function, the Commissionerate is divided into different branches and field formations as explained under the heading 'Administrative Set Up'. Service Tax as provided in Chapter V and Chapter VA of Finance Act, 1994, read with other set of rules for implementation of statutory provisions, is also administered by Central Excise Commissionerate.

The 'Range Office' is the first office of contact between trade and industry and the Department. The assessment of the duty is done by the assessee himself and he pays duty either through the 'Account Current' maintained by him or through credit of duty available with him in the CENVAT account. The scrutiny of the assessment is done by the Range staff on the basis of prescribed returns filed by the assessee. The returns are filed quarterly by units in the small scale sector and monthly by other units. If there is any short payment or non-payment of duty by the assessee, a show cause notice is issued to the assessee. Apart from the assessment work, the Range officials also check the correctness of a few statutory declarations filed by specified assessees, viz. Annual Financial Information Statement, declaration filed with respect to registration of unit or declaration of premises or warehouse etc. The Range officials also check the consignments for export and issue certificates for the quantity and quality of the goods to be exported.

The work of a group of Ranges is supervised by Divisional officer. He may be in the rank of a Deputy Commissioner or an Assistant Commissioner. The Divisional head has certain statutory obligations as prescribed under Central Excise Act & Rules , Finance Act, 1994 and also under Customs Act, 1962 in respect of units working under 100% EOU/STP/EHTP Scheme. He also grants certain permissions under the various Rules. The divisional head is responsible for proper compliance of Central Excise & Service Tax laws and procedure within his jurisdiction. The divisional head also has quasi-judicial function, viz. adjudication of cases falling within his competence.

The work of all the Divisions is supervised by the Commissioner with the help of Additional Commissioners, Joint Commissioners, Deputy Commissioners / Assistant Commissioners and other subordinate officers.

The Anti-Evasion branch of the Headquarters is responsible for collection of intelligence about evasion of duty/tax and takes effective steps to thwart any attempt at that. The officers from audit branch visit the assessee to conduct thorough scrutiny of their financial records to ensure that duty payable by them has been paid correctly and on or before the prescribed date.

In order to ease the difficulties being faced by the trade while dealing with the number of documents, the department also made move towards computerization. As a result the applications like SERMON/SACER/ SAPS/STREMS were introduced in Central Excise & Service Tax and EDI system was adopted in Customs formations. The Department has now become a facilitator to the trade. The implementation of ACES (Automation of Central Excise and Service Tax) is another milestone towards such facilitation.

The Automation in Central Excise & Service Tax (ACES) has been rolled out across the Commissionerate. It is a second generation of software which has been developed to replace the current applications viz. SERMON/SACER/SAPS/STREMS used for capturing the returns & registration details.

The ACES has a number of advantages for the assesses. It facilitates online registration or its amendment, online filing of returns, claims and intimations etc. The assesses can track the status of their claims, reply to Show Cause Notices, file appeal with Commissioner(Appeals) online, view Order-in-Originals etc. The ACES application also provides single source of information on all their transactions related to Excise & Service tax, including duty payment through Cash/ CENVAT, running bond accounts maintained for import & export of goods etc.