In a letter to the FA governing council, Clarke commented on the future the of Premier League and Football League, with the possibility of top flight games being played without fans into the 2020/21 campaign.
He said: "The reality is that we just don't know how things are going to pan out.
"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 explained the FA's executive team are "building out different scenarios that we might potentially face as a result of the pandemic".
He also suggested it would be "sensible" to look at a budget cut of £75 million.
He added: "In a worst-case scenario, this would be necessary for the next four years to offset a £300m deficit.
"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."