Mehrishi succeeded Shashi Kant Sharma, who demitted office on Friday, officials said.
President Ram Nath Kovind administered the oath of office and secrecy to Mehrishi (62) at a function in Rashtrapati Bhavan, which was attended by Vice President M Venkaiah Naidu and Prime Minister Narendra Modi among other dignitaries, they said.
According to the officials, Mehrishi's appointment was recently cleared by the government.
Mehrishi, a 1978 batch (retired) Indian Administrative Service (IAS) officer of Rajasthan cadre, completed his two- year fixed term as the home secretary last month.
Mehrishi will have a tenure of about three years.
The CAG is appointed for a term of six years or till the incumbent attains the age of 65 years, whichever is earlier.
As a constitutional functionary, the CAG is primarily entrusted with the responsibility of auditing the accounts of the Union government and of the state governments.
CAG reports are laid before Parliament and legislatures of the states.
Mehrishi, who hails from Rajasthan, holds Master of Business Administration degree from the University of Strathclyde, Glasgow (UK).
Mehrishi has held several posts in both his state cadre Rajasthan and in the Centre.
Before his appointment as the home secretary, he worked as economic affairs secretary and chief secretary of Rajasthan.
Mehrishi has also worked as secretary in departments of chemicals and fertilisers, and Overseas Indian Affairs.
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