Leeds had secured the support of their next Championship opponents at the ground, Southampton, Barnsley and Hull City, but League rules state that the measurements of a club's pitch must be registered before the start of each season.
Clubs have the right to apply to the Football League's executive for permission to alter their pitch size, but a spokesman confirmed that United would risk a misconduct charge if they proceeded with their plans without the executive's written consent.
Wise says he was "baffled" by the League's insistence, and admitted his long-term plans for United would be better suited to a smaller pitch.
Wise inherited a squad with the worst defensive record in the league and a tighter field would have aided his attempts to shore up a backline which had conceded 13 goals in eight league games before the clash with Colchester.
Wise said: "Unfortunately they won't let me do it, and I don't understand why. We asked the four teams we're playing at home if it was possible, and they didn't mind. None of them objected to it.
"I'm baffled by the reasons why they've turned this down. They haven't explained it to me properly, they've just said 'these are the rules and you're not allowed to change the pitch'.
"There's a maximum and a minimum and we tried to get it to the minimum. I said 'a new manager has come in, and a new manager has new ideas. I'd just like to shorten the pitch.'
"But sometimes you know how awkward they are and they've been awkward."