The history of the Office of the Accountant General, Meghalaya dates back to 1910 when the Office of the Comptroller, Assam was established at Shillong. It gained the status of an Accountant General’s office in 1952 and functioned as a composite Audit and Accounts Office of the then undivided State of Assam. Consequent on the States of Nagaland, Tripura and Manipur being carved out of the State of Assam and with the setting up of Accountants General offices in the state capitals of these three States, the jurisdiction of the Accountant General’s office at Shillong was limited to the territory of the State of Assam. Following the formation of the State of Meghalaya out of the State of Assam in January 1972, the Office of the Accountant General, Assam at Shillong was bifurcated into the Office of the Accountant General, Assam and Office of the Accountant General, Meghalaya, Arunachal Pradesh and Mizoram. Both these offices functioned with their headquarters at Shillong.

As a sequel to the restructuring of the Indian Audit and Accounts Department in March 1984, the following four Accountants General offices were created out of the two existing Accountants General Office at Shillong, viz., Offices of the (i) Accountant General (Audit), Assam (ii) Accountant General (A&E), Assam (iii) Accountant General (Audit) Meghalaya, Arunachal Pradesh and Mizoram and (iv) Accountant General (A&E), Meghalaya, Arunachal Pradesh and Mizoram.

In course of time, the two offices of the Accountants General, Assam shifted from Shillong to Guwahati.

Accountants General offices for the State of Mizoram and Arunachal Pradesh were set up at Aizawl and Itanagar in June 2007 and July 2008 respectively following which the Office of the Accountant General (Audit), Meghalaya, Arunachal Pradesh and Mizoram at Shillong was renamed as the Office of the Accountant General (Audit), Meghalaya.

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