The NCTTCA Secretariat comprises of Specialised Technical Programmes with the mandate to conduct research and advocacy on transport infrastructure issues and promote investment in infrastructure projects in association with development partners such as development finance institutions and national governments.

The NCTTCA Technical programmes include:

1. Transport Policy and Planning Programme with the objective to achieve uniformity in transit transport policies and regulation across Member States; enhance policy harmonization; maintain a transport database and integrate relevant cross-cutting issues.
2. Customs and Trade Facilitation programme to remove non-tariff barriers to trade and reduce the cost of doing business.
3. Infrastructure Development and Management programme to improve performance of infrastructure and facilities; develop sustainable investment schemes and establish mechanisms for management and maintenance of the corridor infrastructure.
4. Private Sector Investment Promotion programme to enable policy and legal framework for the promotion of private sector participation in public infrastructure development through various ways, including Public Private Partnerships (PPP); adopt marketing strategies to enhance PPPs and enable the private sector to participate in policy-making.
5. Monitoring and Evaluation programme to facilitate joint planning and monitoring of activities, identification of crosscutting themes and capacity building needs to link all other programmes.