The Sivagiri Mutt is located at Varkala in Kerala, the final resting place of 20th century saint-reformer Sree Narayana Guru who preached the message of unity.
"Swami Prakashananda blessed the Prime Minister on behalf of the Sivagiri Mutt," an official release said.
"It was great meeting Swami Prakashananda, Head of Sivagiri Mutt, Kerala," Modi tweeted.
He had visited the Sivagiri Mutt in April 2013 as well, when he was chief minister of Gujarat and launched a mobile library of the Mutt at a function at Varkala.
Amid criticism from CPI-M in Kerala at time that the monks of the Mutt were trying to 'saffronise' the spiritual institution, Modi had then said that though spiritual leaders and reformers played a key role to eradicate stigmas in society, "political untouchability" was increasing in the country.