Mohan Bhagwat heads the Rashtriya Swayamsevak Sangh (RSS), which means "National Volunteer Organisation". It's affiliated with the ruling Hindu-nationalist BJP party, which has been accused of not doing enough to stop persecution against Christians and other minorities in India.
He said: "Mother Teresa's service would have been good. But it used to have one objective, to convert the person, who was being served, into a Christian.
"The question is not about conversion but if this [conversion] is done in the name of service, then that service gets devalued.
"But here [at RSS], the objective is purely service of poor and helpless people."
Mr Bhagwat's comment comes after a string of attacks on churches in Delhi, including an arson attack which destroyed the entire inside of a church in the east of the capital.
Mother Teresa was a Catholic nun who set up the Missionaries of Charity in India, a religious order which provides food, accommodation, healthcare and education to the poor.
She received the Nobel Peace Prize in 1979 for her work in the country, and was beatified as "Blessed Teresa of Calcutta" by the Vatican. In 1999 Americans named her the Most Admired Person of the Century in Gallup poll.