The decision to bar Shaddad, says the government, is in line with Sudanese law which says a candidate cannot run for a third term without holding an international football job recognised by the sports ministry.
FIFA strongly objects to any government interference in football and only last month threatened to expel Nigeria after President Goodluck Jonathan banned the national team from international football following the country's first-round exit at the World Cup.
"Any election without respecting the SFA (Sudanese Football Association) statutes and/or under governmental interference will not be recognised by FIFA," FIFA said in a statement sent to Reuters. "In addition, such interference may lead to sanctions such as suspension or expulsion."
FIFA has written to the the Sudan government's Sports Commission to voice its concerns.
