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 (Thrissur), Palghat (Palakkad) and Malappuram.  In July 1949, these two States were merged as the State of Travancore-Cochin.  Shri PN 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 26 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 (Audit) was entrusted with the audit of transactions of the Central Government offices in Kerala and the State Government and the Accountant General (Accounts & Entitlement) was entrusted with the accounting and entitlement functions of the State Government. 

In 1989, the office of the Accountant General (Audit) was divided into O/o the Accountant General (Audit-1) and O/o the Accountant General (Audit-2).  However, the post of the Accountant General (Audit-2) was gradually discontinued and thus, O/o the Accountant General (Audit-2) ceased to exist.  On 14 Feb 1991, Shri RS Gopalan, first Principal Accountant General in Kerala, took charge and the office was known as O/o the Principal Accountant General (Audit).  Since then, the office was titled as O/o the Principal Accountant General or O/o the Accountant General depending on the officers posted.

In October 2009, the office was restructured into O/o the Principal Accountant General (Civil & Commercial Audit) and O/o the Accountant General (Works, Forest & Receipt Audit).  With effect from 1 July 2011, O/o the Senior Deputy Accountant General (Local Bodies Audit & Accounts) functioning since 13 September 2004 for the exclusive audit of Local Self Government Institutions was upgraded as O/o the Accountant General (Local Bodies Audit & Accounts).

With effect from 1 April 2012, these three offices were restructured into two offices following sector-wise audits.  One was titled as Office of the Principal Accountant General (General and Social Sector Audit), which was 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.  The other was named as Office of the Accountant General (Economic and Revenue Sector Audit), which was 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 then 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.  

On 15 May 2020, the offices were again restructured based on cluster-based audit.  Accordingly, the O/o the Accountant General (General & Social Sector Audit) was renamed as the O/o the Accountant General (Audit-1).  This office is responsible for audit of cluster of Government Departments such as (1) Health and Welfare, (2) Education, Skill Development & Employment, (3) Rural Development, (4) Agriculture, Food & Allied Industries, (5) Water Resources, (6) Urban Development, (7) Law and Order and (8) General Administration.  The O/o the Accountant General (Economic & Revenue Sector Audit) was renamed as the O/o the Accountant General (Audit-2.), responsible for audit of the other eight clusters.  With effect from 1 January 2021, both the offices were titled as O/o the Principal Accountant General (Audit-1) and O/o the Principal Accountant General (Audit-2).

The cadre control of all the staff members posted in offices of the Principal Accountant General (Audit-1), the Principal Accountant General (Audit-2) and the Director General of Audit (Central), Chennai, Branch Office Kochi lies with O/o the Principal Accountant General (Audit-1), Kerala. 

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