The Scottish Football League is rejecting the Scottish FA's offer of help in the row over league change in order to work on its own plans.
The SFA offered to "get involved" in the debate after St Mirren and Ross County vetoed proposals at a Scottish Premier League meeting on Monday.
SFL chief executive David Longmuir is seeking "an alternative way forward".
And he added: "We would like to exhaust all possible avenues of a solution within the clubs themselves."
The plans, which would have included the five principles of a single league body, fairer financial distribution, introduction of play-offs, parachute payments and a pyramid below the Third Division, needed an 11-1 majority from top flight clubs before being sent to the SFL.
The SPL board has since invited SFA chief executive Stewart Regan and president Campbell Ogilivie to hold talks in a bid to achieve consensus but the SFL wants to discuss the matter internally.
A statement from Longmuir read: "The board of the Scottish Football League wishes to convey its thanks to the governing body for its offer of assistance at this time.
"We are, however, currently working with SFL clubs in all divisions with a view to agreeing an alternative way forward which builds on the five core principles.
"We would like to confirm our continued commitment to those principles.
"We are also very keen to share our proposals with the SPL and the SFA as soon as practical.
"We therefore respectfully wish to ask the SFA to work with us at this time, whilst we progress our proposals."
First Division clubs are due to meet on Monday to talk over the impact of the SPL veto on a new 12-12-18 league set-up.
A breakaway from the SFL to join the SPL is expected to be on the agenda but such a venture would require backing from 11 top flight clubs.