Office of the Chairperson – supports the HUDCC Chairperson in his/her task of providing overall direction to carry out the functions of the agency as well as in his/her capacity as Chairman of the Board of the Key Shelter Agencies.​               

Office of the Secretary General – provides technical and administrative support to the Secretary General (SG) in the implementation of policies and measures approved and directed by the Chairperson and in managing the day-to-day operations and affairs of the HUDCC.          

Offices of the Deputy Secretary General - tasked to oversee the functions of the different operating groups and assist the Secretary General in managing the day-to-day operations of HUDCC.

Policy Development, Legislation and Special Projects Group (PDLSG) – formulates and reviews policies, plans, programs, and guidelines related to housing and urban development.

Coordination, Monitoring and Evaluation Group (CMEG) – assists in the formulation of sector plans, monitors and evaluates the performance of shelter agencies and consolidates the overall accomplishments of the housing sector.

Legal,  Anti-Squatting and External Affairs Group (LASEAG) – provides legal and counselling services relative to the functions of the HUDCC, including the review of contracts, handling of all litigation cases filed for and against HUDCC; oversees the curtailment of nefarious and illegal activities of professional squatters and squatting syndicates; and provides overall public relations, information an​d assistance to external clients of HUDCC.

Asset Reform Group (ARG) – provides overall direction in the optimum utilization of idle government properties, particularly the proclamation of these properties for housing and secure tenure, and conducts complete staff work on all requests for proclamation of idle government lands for socialized housing prior to submission to the DENR and Office of the President for approval. It is also responsible for overseeing the development of proclaimed areas, where HUDCC is the administrator, as well as monitoring the implementation of other proclamations administered by other agencies.

Community Development Group (CDG) – facilitates the implementation of a comprehensive community development framework that will enable newly formalized poor owners and small entrepreneurs to form new productive ties and networks with each other and with other sectors.

Regional Operations Group (ROG) – oversees the implementation and ​monitoring of housing policies and programs in the regions, through linkages with concerned agencies and organizations at the field level.

The HUDCC has offices in the following regions:  Baguio City serving Regions I, II and CAR; Legazpi City for Region V; Iloilo City for Region VI; Cebu City for Regions VII and VIII; Zamboanga City for Region IX; Cagayan de Oro City for Regions X, CARAGA and a portion of ARMM; and Davao City for Regions XI and XII and a portion of ARMM.  The concerns of Regions III, IV-A and IV-B are directly handled by HUDCC Central Office.​

Administrative, Finance and Knowledge Management Group (AFKMG) – provides effective and efficient administrative and financial support to the HUDCC through human resource development; systematic planning and budgeting; acquisition, maintenance and disposition of assets; and information system management.