Chief Justice of the Meghalaya High Court Uma Nath Singh administered the oath of office to Shanmuganathan at a solemn ceremony attended by Chief Minister Mukul Sangma and most of his cabinet colleagues.
Shanmuganathan was appointed as the new Governor on May 12.
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Meghalaya was without a permanent governor for over four months.
Keshari Nath Tripathi, the West Bengal governor, had been taking the charge since the former incumbent K K Paul was removed from the post in January this year.
Shanmuganathan is a post-graduate and an M Phil in political Science.
He joined the Rashtriya Swayamsevak Sangh in 1962 and later joined Bharatiya Janata Party and served in many party positions.
He has been in-charge of the Defence, Research and Documentation and Overseas Friends of BJP Cells.
A prolific writer, the BJP leader had written three books relating to culture and social aspects in Tamil.