The man who has bought the Yorkshire club on three occasions will not be allowed to railroad rules which have governed 41 other clubs in administration.
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Bates has been criticised by Leeds fans
Bates, chairman of Leeds United 2007 and the man who took the club into administration in early May with debts of £35million, must reach an agreement with the club's creditors before the League will sanction their opening fixture at Tranmere Saturday week.
Bates, through the club's administrators KPMG, had been hoping to persuade the League to hand over the socalled golden share - effectively the stamp of membership of the Football League - by persuading them that Leeds' situation constituted an exceptional circumstance.
However, the League rejected that course of action at a four-hour meeting with the administrators and Leeds United 2007 on Tuesday.
Instead, they requested the administrators to revive the Company Voluntary Agreement (CVA) which Bates had dropped after it was challenged by the Inland Revenue over an unpaid £7.7m tax bill.
There was no open threat from the League to former Chelsea chairman Bates to abide by the rules, but it is clear the League's patience is running thin.
Chairman Lord Mawhinney said: "Will Leeds start the season? I haven't got a crystal ball although I'm an optimist, not a pessimist.
"Part of our policy is to do whatever we can that is within the rules to ensure the continuation of our member clubs through administration.
"But my framework on behalf of all 72 clubs is to administer the regulations that all 72 of them have agreed to be bound by.
"That's what we're doing, although we have no control over the administrators, who are answerable to the law of the land.
"We have got to resolve this issue and we've got to resolve it soon because the season starts soon.
The normal way to resolve this is for the CVA to go through. Once it has, there is a legal agreement as to what all the unsecured creditors get.
"If the CVA could be reconstituted then Leeds United, in terms of the old company, could start the season."
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