The Custom House, Mumbai existed much before, 1878 when the Sea Customs Act, 1878 was enacted, which was subsequently replaced by the Customs 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 areas were a part of functions of the Custom House including the clearance of passengers at the International 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 Central Excise, Bombay and the Gold Control.

The Customs activities at the International Airport and Air Cargo Complex continued to be with the Mumbai Custom House until 1983 when a separate Collectorate of Customs, Mumbai Airport was set up.  In view of the remarkable increase in air traffic with the introduction of wide bodied aircrafts and for effective control of day to day administration at the International Airport and Air Cargo Complex, this Collectorate was divided into Collectorate of Customs, International Airport and Collectorate of Customs, Air Cargo Complex in 1997.

In November 2002 the Collectorate of Customs, Air Cargo Complex was bifurcated into a Commissionerate of Customs for Imports and a Commissionerate of Customs for Exports under the jurisdiction of the Chief Commissioner of Customs, Mumbai Customs Zone – II which comprised of the Seaport of Nhava Sheva and Air Cargo Complex, Mumbai.  With effect from 26^th July 2007 the Commissionerate of Customs (Import) and the Commissionerate of Customs (Export), ACC were administratively re-aligned and taken out from the jurisdiction of Chief Commissioner of Customs, Zone – II and re-aligned with its sister Commissionerate at the International Airport and brought under the jurisdiction of the Chief Commissioner of Customs, Mumbai Zone – III. 

Mumbai Customs Zone – I comprises the Import, Export and General Commissionerates at New Custom House, Mumbai. Mumbai Customs Zone - II  comprises the Jawaharlal Nehru Custom House (Import and Export Commissionerates). Mumbai Customs Zone - III comprises Air Cargo Complex (Import and Export), Airport Commissionerate and Commissionerate of Customs (Preventive), Mumbai.