The FA will now discuss the situation with other leagues in a bid to establish the best way to proceed with the complaint.
Chaiman Ken Bates has already rejected a £200,000 (€295,346) offer from Chelsea, calling it 'insulting'.
The FA and the two leagues must also decide whether any disciplinary action should be taken against Chelsea if they are found to have broken the rules.
The two who got away... and the one who stayed;
Tom Taiwo was born in Bradford and joined Leeds' youth set-up aged nine in October, 1999. His England Under-16 debut came in the Sky Sports Victory Shield tournament last Autumn.
York-born Michael Woods joined Leeds in September 1999, at the age of 10. Along with then club-mates Taiwo and Daniel Rose, he was included in the England Under-16 squad at a training camp at Lilleshall last summer.
Woods and Taiwo signed scholarship forms with Chelsea on April 10 this year.
Daniel Rose signed for United in 2002 at the age of 11 and last season represented England at Under-16s level and played for Leeds Under-18s. He turned down Chelsea to stay at Elland Road.