He was 94 and is survived by his wife Kamala Raja.
The Zamorins, the hereditary royal title, once ruled the "Malabar" region of Kerala.
Manavikraman Raja was anointed the Zamorin after the death of P K S Raja in March last year.
He was in Indian Foreign Service and retired in 1980 as Third Secretary from Indian Embassy in the erstwhile Czechoslovakia.