Sayed Abdel Latif spent months in a low security detention centre in South Australia, even after authorities learned he was subject to the Interpol red notice.
Interpol says after consultation with its Cairo bureau, charges were removed from the red notice - including premeditated murder, and possession of firearms and explosives without a permit.
It says the only remaining charges relate to membership of an illegally formed extremist organisation.
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The Australian Federal Police says it's written to Interpol seeking more information on the changes.
Monash University international law and human rights expert Dr Patrick Emerton says security notices from agencies such as Interpol don't take into account whether an asylum-seeker poses a threat to Australia.
He told Darren Mara that by relying on Interpol notices when processing asylum-seekers, Australian authorities risk rejecting genuine asylum claims.
