The Accounts Section manages all financial operations of the Department. This includes the processing and disbursement of salaries to employees, processing of various bills including settlement of bills for expenditure incurred by the office, maintenance of cash books and financial registers, reconciliation of accounts with the Pay and Accounts Office, and preparation of budget estimates and expenditure statements. The section manages matters related to pensions and addresses associated grievances of employees. In addition, it handles statutory compliances such as GST filings, income tax, and TDS deductions and records. This Section facilitates internal and local audits, ensuring that all financial transactions adhere to prescribed rules and regulations. The Drawing and Disbursing Officer (DDO) functions within this section and is responsible for ensuring compliance with all Government financial rules and audit requirements.

The Hindi Section (Rajbhasha Anubhag) is responsible for the implementation of the Official Language Policy of the Government of India within MMD Chennai and its subordinate offices. The section oversees the progressive use of Hindi in official correspondence, prepares quarterly and annual progress reports on Official Language implementation, coordinates with the Town Official Language Implementation Committee (TOLIC), arranges Hindi workshops and training programmes for staff, and ensures compliance with the Official Languages Act, 1963 and the Official Language Rules, 1976. All bilingual requirements for official communications, signage, and public-facing content are managed through this section.

The Ship Registration and Survey Section is the operational core of the Department's vessel safety mandate. It conducts all statutory surveys of ships, including initial, intermediate, annual, and periodic surveys as required under SOLAS, MARPOL, and the International Load Line Convention. The section handles surveys for the registration of new and second-hand vessels, conducts IMDG Class I cargo handling inspections, and carries out port inspections including ISPS and NSPC compliance. It is also responsible for casualty investigations and inspection of workshops covering LSA, FFA, and EPIRB equipment. Surveyors carry out field inspections of vessels and submit detailed reports on any deficiencies observed, with follow-up until rectification.

The section is also responsible for Port State Control (PSC) inspections of foreign-flag vessels calling at Indian ports and Flag State Inspections (FSI) of Indian-flag vessels, petroleum licence inspections, towing inspections, and all ISM, ISPS, and MLC audits within the Chennai maritime district. The nomination and allocation of surveyors for these duties is coordinated through this section in consultation with the Principal Officer and the Dy. Chief Surveyor.

The Engineering Examination and Certification (EAC) Section conducts STCW examinations and assessments for all engineering grades of competency, from Marine Engineer Officer Class IV (Officer in Charge of an Engineering Watch) through to Class I (Chief Engineer). The section manages the complete examination cycle: scheduling, invigilation, assessment, compilation and declaration of results, and issuance of Certificates of Competency (CoC), issuance of Electro-Technical Rating (ETR) CoP and UK CoC endorsements. It also handles Dangerous Cargo Endorsements (DCE) for oil, chemical, and gas tanker operations, IGF Code endorsements (basic and advanced), Electro-Technical Officer (ETO) assessments, NCV (Near Coastal Voyage) engineering certifications, Type Rating Certificates, and age dispensation applications for the engineering stream.

The Nautical (Deck) Section conducts STCW examinations for all deck grades of competency, including Second Mate Foreign-Going, First Mate Foreign-Going (Phase I and Phase II), and Master Foreign-Going. The section manages the full assessment and certification pipeline for the nautical stream: written examinations, oral assessments, preparation and declaration of results, issuance and re-validation of Certificates of Competency, and processing of Certificates of Endorsement for foreign-issued COCs. It also handles GMDSS (Global Maritime Distress and Safety System) operator examinations and certifications, NCV deck certifications, and Mate/Master certifications for fishing vessels and issuance of Skipper grade I and II of fishing vessel operating within the Chennai maritime district.

The Legal Cell handles all court cases and quasi-judicial proceedings wherein the Mercantile Marine Department is a party, or where the Directorate General of Shipping is involved based on their directions. This includes liaising with Government Counsels, preparing para-wise comments, preparing counter affidavits, tracking hearing schedules across the Madras High Court and subordinate courts, filing periodic status reports to DGS, and ensuring compliance with court orders within stipulated timelines and it also undertakes the drafting of Show Cause Notices (SCNs) and speaking orders. The cell also handles legal matters arising from shipping casualty inquiries, detention of vessels, and appeals under the Merchant Shipping Act. All court case files are compiled and monitored by the designated Nodal Officer for court cases in coordination with the Dy. Chief Surveyor.

The Maritime Training Institutes (MTI) Section exercises regulatory supervision over all DG Shipping-approved maritime training institutes within the Chennai maritime district and ensure compliance with STCW Convention. The section conducts scheduled and surprise inspections of MTIs to verify compliance with the standards prescribed by the Directorate General of Shipping, processes applications for new MTI approvals and renewals, handles matters relating to the Comprehensive Inspection Programme (CIP) approval system, and monitors adherence to faculty qualification requirements, infrastructure standards, simulator facilities, and student intake norms. Inspection reports and compliance recommendations are forwarded to DGS for further action.

The Principal Officer's Secretariat provides secretarial and coordination support to the Principal Officer, MMD Chennai. The section manages the Principal Officer's calendar, coordinates appointments, meetings, and visits by officials, dignitaries, and industry stakeholders through the Visitor Access Management System (VAMS). It also handles all incoming correspondence addressed to the Principal Officer, routes files to relevant sections with appropriate markings and instructions, coordinates with DGS headquarters and subordinate offices on urgent matters, and manages outstation tour arrangements. The Sr. PA to the Principal Officer monitors the common email (chennai-mmd@gov.in) and submits all incoming communications to the PO or the senior-most Surveyor for information and allocation of work.