Newport asked the organisation to sanction the number eight's transfer to the English Premiership club but the WRU said the club must fulfil a contractual agreement which ensures the player remains with them at least until the end of season 2015/16.
"We stand alongside the Regions in our commitment to try to keep the best Welsh qualified players here in Wales where they can compete for international honours," WRU chief executive Martyn Phillips said in a statement on Tuesday.
"Although there are circumstances under which moves out of Wales by experienced players can be sanctioned, Taulupe's (Toby) status as a player and importance as a role model means we would like him to be playing his rugby here."
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Faletau, 24, has won 52 caps for Wales and was a key member of the side that reached the World Cup quarter-finals this month.
(Reporting by Justin Palmer; editing by Tony Jimenez)
