The former First Minister was highly critical of the governing body as the second and final part of his review of Scottish football, dealing with structures, leadership and governance, was published.
He said: "I want the SFA to be far more confident, far more assertive, giving more leadership to the game. The SFA could be a much bigger force in the Scottish game than they are. At the end of the day, make decisions quicker, be more streamlined, be more effective, be more efficient."
McLeish also wants the SPL and SFL to combine to create one league structure, the introduction of a pyramid system and a complete overhaul of the SFA's structures, organisation and decision-making processes.
He said: "Scotland is not big enough in football terms to have two institutions. I have suggested we merge both of them so there is dialogue and consultation, but also to share a lot of costs.
"This is not an auspicious time to be reconstructing the leagues but there is demand for change and it has to be thought out.
"I put in the recommendation that the option is ten or 14 teams. There is a debate to be had here, not just with the SFL, but with the country and the fan-base."