Warehouse operations were among the primary services provided by the Company. In line with the changes in global trade following 1990, where most goods began arriving in containers and being transported in containers, such warehouses have been returned to the Kolkata Port. The warehouses operated by the Company in the major customs points of Nepal, namely Biratnagar and Kakarbhitta customs areas, have also been transferred to the Nepal Intermodal Transport Development Board in accordance with the directives of the Government of Nepal after the construction of ICD or ICP in those areas. The warehouses located in the old Birgunj customs area under the Company's ownership have largely remained closed due to the shift of cargo flow towards the dry port, and are in the process of being transferred to the customs office. Similarly, the warehouse located in Raxaul is also affected by the dry port but continues to operate at minimal capacity. Currently, the Company primarily operates air cargo warehouses at Tribhuvan International Airport and other international airports under a revenue-sharing contract agreement with the Civil Aviation Authority of Nepal. Although agreements have been made for air cargo operations at Gautam Buddha Bhairahawa and Pokhara International Airports as well, they have not yet commenced operations. Likewise, pursuant to the Transit Treaty, land leased from the Government of India—measuring 53,518 square feet (4,972 square meters) on CGR Road in Kolkata and 75,385 square feet (6,985 square meters) at Haldia Dock Port—can also be utilized for cargo consolidation and warehouse management. Plans are in place to emphasize commercial utilization based on a study of the commercial feasibility of that land. However, the lease for the 53,518 square feet land on CGR Road in Kolkata has not been renewed by the Government of India since April 2023, and a request has been made for an alternative plot in its place.

Apart from the above open land spaces provided by the Government of India, NTWCL has been operating its warehousing services also at the following transit heads in order to facilitate the transit cargo of Nepal.'