The Kolkata Customs Zone is headed by Chief Commissioner of Customs. There are four Commissionerates, namely, Commissionerate of Customs (Port), Commissionerate of Customs (Airport & ACC), Commissionerate of Customs (Preventive), West Bengal and Commissionerate of Customs (Appeals) each having it's own jurisdiction headed by a Commissioner.

The subordinate cadres consist of the Appraising wing which is chiefly entrusted with the assessment and collection of revenue and the Preventive wing, which is engaged in anti-smuggling activities. The Ministerial staff help in administration and and accounts related matters.

Commissionerate of Customs (Port) and Commissionerate of Customs (Airport & ACC) have units named Special Investigation Branch (SIB) which is engaged in countering commercial frauds.  Commissionerate of Customs (Preventive) has anti-smuggling wings like Dock Intelligence Unit (DIU), SRI and P&I  and also tasked with operating Land Customs Stations and responsible for Customs border controls.