The Custom House, Mumbai existed much before, 1878 when the Sea Custom Act, 1878 was enacted, which was subsequently replaced by Custom Act, 1962. Initially, the jurisdiction of Custom House, Bombay extended over the port and city limits of Bombay as well as the area in the vicinity of Airport. The anti-smuggling activities in these area were a part of functions of the Custom House including the clearance of passengers at Airport and Cargo at Air Cargo Complex.

During the later half of the sixties, there was a sudden spurt in the smuggling activities and to fight the ever increasing smuggling menace and to strengthen the Anti-smuggling machinery on the west coast, the Commissionerate of Customs (Preventive) was set up in 1970 under a separate Collector of Customs (Preventive) by taking into its fold the Rummaging and Intelligence division of the Custom House and Marine and Preventive division of the Central Excise, Bombay and the Gold Control.

The Customs activities at the Airport and Air Cargo Complex continued with the Mumbai Custom House till 1983 when a separate Collectorate of Customs, Sahar Airport was set up, which was divided into Collectorate of Customs, Airport and Collectorate of Customs, Air Cargo Complex in 1997. This was necessitated because of the remarkable increase in the air traffic with the introduction of wide bodies aircrafts and for effective control of day to day administration at the Airport and Air Cargo Complex. The New Custom House, Bombay was later on divided into three separate Commissionerates in July, 1997 namely Commissionerate of Customs (Imports), Commissionerate of Customs (Export Promotion) and Commissionerate of Customs (General).

The import Commissionerate deals with the appraising and examination of import cargo. The Commissionerate of Customs (Export Promotion) deals with assessment of Export and export related import and examination of export cargo. The Commissionerate of Customs (General) deals with the land, building, vehicles, estate, accommodation, MCD, audit, cash, accounts, computers, CIU, Vigilance, UB Center, Personnel and Establishment, Customs revenue control laboratory and Preventive Service Organization including Gr. 'D' Estt. and CHA.

With effect from November 2002, there is a separate Commissionerate of Customs for Imports and a separate Commissionerate of Customs for Exports at Air Cargo Sahar. After cadre restructuring, there are now three custom zones in Mumbai. The Import and Export Commissionerate at Custom House Mumbai and Commissionerate of Custom (general) comes under Mumbai Custom Zone I. Nhava Sheva Custom House (Import and Exports) and Air Cargo Complex Sahar (Both Import Commissionerate and Export Commissionerate) now comes under Mumbai Custom Zone II. Airport Commissionerate and Commissionerate of Customs (Preventive) Mumbai comes under Mumbai Custom Zone III.