The former England full back played for Fulham after signing on loan from Aston Villa, following an earlier nine-game spell at Nottingham Forest.
But Shorey and Fulham are backed by the FA, the Premier League and the Football League, all of whom classify his time at Forest as an emergency loan.
A FIFA spokesman said: 'FIFA are concerned about the system of emergency loans in general and have approached the Football Association on various occasions in the past regarding this. FIFA will be contacting them again in order to obtain clarification with regard to this issue.'