A proposal to expand the Nationwide play-offs from four to six teams was forced off the agenda at the Football League's Annual General Meeting on Thursday.
Play-off changes are on hold
Crystal Palace chief executive Phil Alexander had suggested the controversial change.
But both the Premiership and Football Association wrote in to express their reservations, necessitating further debate on the subject.
"The clubs referred the play-off situation back to the League board for further consideration after reservations expressed by the FA and Premier League," said spokesman John Nagle.
The League also deferred proposals to impose punishments on clubs who fall into administration.
We have the best second tier league in the world - with far higher gates than France, Italy, Germany or Spain
Sir Brian Mawhinney
Football League Chairman
They will now be discussed at an Extraordinary General Meeting in September after opposition from Division One clubs.
But minor structural changes were approved at Thursday's meeting, which was held at Gillingham's Priestfield Stadium and attended by 80% of Football League clubs.
Those passed included:
A proposal to lower the stadium entry requirements for clubs promoted from the Nationwide Conference from 6,000 to 4,000 was passed unanimously.
A proposal for all new playing contracts to specify the level of salary in the event of a player being promoted or relegated between the divisions was also agreed.
The League agreed to introduce a First Division managing director and a sales and marketing director to work alongside the current operations director.
League chairman Sir Brian Mawhinney broke a one-year deadlock by agreeing to the plans for the managing director.
He said: "We have made a breakthrough to the stalemate and we received the overwhelming endorsement of the representatives.
"We can now take our eyes off the internal management of the League and concentrate on moving forward."
First Division clubs have been pushing for a more prominent voice since the collapse of ITV Digital, which plunged many of them into financial chaos.
And Mawhinney aims to make sure that Division One gets a make-over to underline its status as "the best second-tier league in the world".
"We will be taking professional advice aimed at re-branding
the Football League," he added.
"We have the best second tier league in the world - with far higher gates than comparable leagues in France, Italy, Germany or Spain and we want to enhance our standing.
The Second and Third Divisions will be represented by a deputy operations director, and an independent non-executive director will be added to the League board to add a voice from outside the football world.