Acharya will hold charge in both the northeastern states.
Chief Justice of Gauhati High Court, Justice Ajit Singh administered the oath of office to the new Governor in a simple function organised at the Darbar Hall of the Raj Bhavan, here.
Chief Minister Pema Khandu, his cabinet ministers, members of state legislative assembly, chief secretary in-charge Satya Gopal, principal secretary to the home department, other senior officers and public leaders were among those who attended the function.
Shanmuganathan, a veteran RSS pracharak from Tamil Nadu, had tendered his resignation on Republic Day facing sexual harassment charges.
Nearly 100 Raj Bhavan staff in Shillong had petitioned President Pranab Mukherjee, Prime Minister Narendra Modi and Union Home Minister Rajnath Singh seeking their intervention to remove Shanmuganathan and restore the dignity of Raj Bhavan.
The employees had alleged that Shanmuganathan had "seriously compromised" the dignity of the Raj Bhavan and made it a 'young ladies club'.