He was bed-ridden for some time following age-related ailments, family sources said.
He is survived by wife Devaki, son Mohanaru and daughters Mallika and Devika.
Kandararu Maheswararu was the member of the famed Thazhamon family, which has the hereditary right of priesthood at the hill temple, located in Pathanamthitta district.
He had been performing duties as a 'tantri' for many decades at the Ayyappa Temple, where lakhs of devotees throng during the annual pilgrim season.
The nonagenarian priest was not able to travel to the hillock shrine for some time to carry out his responsibilities due to poor health.
Maheswararu also installed idols and performed tantric duties in hundreds of temples in the country and abroad, besides Sabarimala.
The date and time of cremation would be decided later, the family members added.