Deputy Chief of Mission of Embassy of India Jaideep Mazumdar and other senior embassy staff were also present on the occasion at the Rastrapati Bhawan.
Rae, 55, has arrived in Kathmandu on Monday to take up his new assignment as the Indian Ambassador.
He has succeeded Jayant Prasad, who returned to Delhi recently upon completing his tenure.
Prior to his appointment as the Ambassador to Nepal, Rae had served as the ambassador of India to Vietnam.