The offices of the Accountants General, Meghalaya have a history dating 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. With the creation of the States of Nagaland, Tripura and Manipur the geographical jurisdiction of the Accountant General’s office at Shillong was reduced, with the setting up of Accountants General offices in the state capitals of these three States in 1973. In March 1984 the Indian Audit & Accounts Department was bifurcated into the Audit Wing and the Accounts & Entitlement (A&E) Wing and four Accountants General offices, all with headquarters at Shillong, were created, viz., offices of the (i) Principal Accountant General (Audit) Assam (ii) Accountant General (A&E) Assam (iii) Principal Accountant General (Audit) Meghalaya, Arunachal Pradesh and Mizoram and (iv) Accountant General (A&E) Meghalaya, Arunachal Pradesh and Mizoram.

In course of time, the offices of the Accountants General, Assam shifted from Shillong to Guwahati. With the creation of new Accountants General offices for Mizoram at Aizawl and Arunachal Pradesh at Itanagar in April 2006, the two Accountants General offices at Shillong were redesignated as the offices of the Principal Accountant General (Audit) Meghalaya and Accountant General (A&E) Meghalaya.