His body will be sent to Sri Lanka after "discussions with the Sri Lankan government," ministry spokesman Teuku Faizasyah told AFP.
"He died of his illness... We're preparing to send his body to Sri Lanka some time this week," Faizasyah added.
Christian was suspected of suffering from a stomach infection, provincial port health official Endang Syarifuddin said.
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He is one of about 250 ethnic Tamils headed for Australia who have refused to leave their boat in the port town of Merak after they were intercepted off Indonesia in October.
They staged a brief hunger strike and threatened to torch their boat to draw attention to their plight.
Faizasyah said the migrants had prevented Indonesian authorities from boarding the boat to carry out medical inspections.
"Part of the reason we couldn't provide early medical assistance (for Christian) is because they r