Authorities say Gaete was hanging from a rope in an abandoned house in Cusco, Peru.
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His body was discovered after a neighbor had called police to report that someone had committed suicide in the building.
While on the run the cult leader had changed his appearance by cutting his hair and beard.
Interpol has positively identified Gaete by his fingerprints.
Police Gen. Javier Avalos initially told reporters that though Gaete died in an apparent suicide, the cause of death would still have to be officially determined.
Cusco police chief Juvenal Zereceda later told Chile’s La Tercera Newspaper, “There is no evidence of anyone else taking part in his death. All the preliminary evidence indicates this was a case of suicide.”
Ramon Castillo was the subject of an international manhunt for allegedly burning a baby alive on a bonfire in the belief that end of the world was near, and that the child was the ‘Antichrist.’
Sect members says Castillo, who believed himself to be divine, expected the world to end on December 21, 2012.
Four members of the 12-member sect, including the child’s mother, Natalia Guerra, were arrested last week.
Two others turned themselves in last Monday.
International arrest warrants are still out for the remaining fugitives.