Prior to Independence, the princely state of Travancore, with its headquarters at Trivandrum ruled most of South Kerala, while, the princely state of Cochin (Kochi) ruled most of modern Cochin, Trichur, Palakkad and Malappuram. In July 1949, these two states were merged as the State of Travancore-Cochin. Shri P.N.Padmanabha Pillay, who was the Accountant General of Travancore State, continued as the head of the integrated office and the Comptroller of the Cochin State, Shri K.Govinda Menon took over as Senior Deputy Accountant General.

Travancore-Cochin became a Part-B State on 26th January, 1950 and with the federal financial integration that took place in April 1950, audit and accounting functions became the responsibility of the Comptroller & Auditor General of India. The designation of the office was changed to Comptroller, Travancore and Cochin and the then State Accountant General Shri Govinda Menon became the Comptroller.

With the reorganisation of States in November 1956, the new State of Kerala was born, comprising of the erstwhile State of Travancore-Cochin, Malabar District and Kasaragod Taluk. The Office was upgraded to Accountant General’s level in 1960 and Shri S.Vasudevan, the last Comptroller of the Travancore-Cochin State was appointed as the first Accountant General of Kerala.

In March 1982, the office was reorganised into two units, each under an Accountant General, designated as Accountant General I and Accountant General II. Accountant General I was declared the principal audit and accounting officer of the Kerala Government, and made responsible for rendition of monthly accounts to the State Government and the preparation of the Finance and Appropriation Accounts and Audit report (Civil). Accountant General II was entrusted with the audit of state receipts and commercial undertakings.

In March 1984, the office was reorganised into distinct functional categories. The Accountant General (Accounts & Entitlement) was entrusted with the accounting and entitlement functions of the State Government and the Accountant General (Audit) was entrusted with the audit of transactions of the Central Government offices in Kerala and the State Government.

Consequent on a major restructuring with effect from April 2012, Audit offices were restructured into two offices following sector-wise audits.  They are Office of the Accountant General (General and Social Sector Audit), which is primarily responsible for the Audit of accounts of the Departments/ Agencies/ Public Sector Undertakings/ Autonomous Bodies grouped within General and Social Sector in the Government of Kerala; and Office of the Accountant General (Economic and Revenue Sector Audit), which is responsible for the Audit of accounts of the Departments/ Agencies/ Public Sector Undertakings/ Autonomous Bodies grouped within Economic and Revenue Sector in the Government of Kerala.  While these two offices were constituted exclusively for audit relating to the Government of Kerala, audit pertaining to Central Government offices functioning in Kerala was handed over to the region-wise newly formed office titled Office of the Director General of Audit (Central), Chennai with a Branch Office at Kochi.  This Branch Office is responsible for the audit of expenditure and receipt of all Central Government units located in Kerala including Autonomous Bodies. 

In April 2020, Audit Offices were again restructured into Principal Accountant Genera (Audit-I) and Principal Accountant General (Audit-II) and each office is responsible for the Audit of accounts of the Departments/ Agencies/ Public Sector Undertakings/ Autonomous Bodies grouped in the eight clusters each.

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