Chief Controller of Accounts (CCA) is overall in charge of the Budget, Payment & Accounting functions for the Ministry of Agriculture under three departments i.e. Department of Agricultural Research and Education (DARE) Department of Agriculture and Co-operation and Department of Animal Husbandry and Dairying The Secretary of the each Department is the Chief Accounting Authority and performs these functions with the help of Joint Secretary & Financial Advisor and Chief Controller of Accounts.

The Chief Controller of Accounts is the Head of Department of Payment and Accounting Organisation and is assisted by two Controllers of Accounts, one Assistant Controller of Accounts and 13 Sr. Accounts Officers/Pay & Accounts Officers. 

The Payment and Accounts function of this Ministry is performed through 11 Pay and Accounts Offices (PAOs); 4 are situated in New Delhi, 2 in Mumbai, 1 at Faridabad, 1 in Kolkata, 1 in Chennai, 1 at Cochin and 1 at Nagpur as well as an Internal Audit Wing in New Delhi and Cochin. In order to discharge the budget, finance and accounts functions in Director of Plant Protection & Quarantine Storage (PPQS) representative of the CCA is posted in this department as Sr. Accounts officer / Pay & Accounts Officer under the administrative control of the CCA. There are in all about 210 spending units in the Ministry, of which 39 are cheque signing units (CDDOs) and are 171 non-cheque signing units (NCDDOs).