Football Association chairman Greg Clarke has said it is hard to see fans returning to matches “any time soon”.
If the Premier League and Football League resume then those matches will be played behind closed doors.
The Premier League are also preparing for the possibility of playing the 2020-21 season without fans.
“The reality is that we just don’t know how things are going to pan out,” Clarke wrote in a letter to the FA governing council.
“But with social distancing in place for some time to come we do face substantial changes to the whole football ecosystem.
“For example it’s hard to foresee crowds of fans – who are the lifeblood of the game – returning to matches any time soon.”
Clarke said the FA’s executive team has been “building out different scenarios that we might potentially face as a result of the pandemic.”
He also warned a budget cut of £75m will be “sensible” this year.
“In a worst-case scenario, this would be necessary for the next four years to offset a £300m deficit,” he added.
“Clearly that will impact many of our plans as every area of the game will be touched and projects that we all value will be affected.”
‘Clubs rebelling against neutral stadiums’
Top-flight clubs have been told that using up to 10 neutral stadiums will be the only way to complete the season.
Brighton say they are “not in favour” of using neutral venues because it may affect the “integrity” of the league.
Clubs near the bottom of the table feel it is unfair to play in such different conditions when at risk of relegation.
A growing number of Premier League clubs are open to playing the remaining fixtures at neutral venues but with the threat of relegation removed.
The BBC has learned that the Premier League fear between six or seven clubs are opposed to neutral stadiums.
But there is also a sense that within that group there are disagreements over how they want the season to end.
Prime minister Boris Johnson will reveal his “roadmap” out of lockdown on Sunday and that means that the Premier League’s next meeting will be delayed until next week.
The Premier League has been suspended since 13 March because of the coronavirus pandemic but all clubs are committed to playing the 92 remaining fixtures of the 2019-20 season if and when safe to do so.