The outbreak of Covid-19 has seen the Premier League and EFL suspend their campaigns indefinitely – and there is uncertainty if or when they will return.
Clarke also alluded to the financial impact of the pandemic with clubs across the country placing staff on furlough.
In a speech to the FA Council, he said in full: “Football faces economic challenges beyond the wildest imagination of those who run it.
“We face the danger of losing clubs and leagues as finances collapse. Many communities could lose the clubs at their heart with little chance of resurrection.
“In the face of this unprecedented adversity, all the stakeholders within the game from players, fans, clubs, owners and administrators need to step up and share the pain to keep the game alive.
“Everyone should understand that the Premier League clubs are not immune from the impact of this and whilst they are impacted to different degrees depending on their cost base, the potential overall financial impact is huge.
“We must have a plan to ensure that English football is not decimated should this season be lost and next season blighted. We hope we do not need this plan as we are all determined to finish the professional football season, however we would be fools not to develop such a contingency plan. Those that lost their clubs because English football did not rise to the challenge would rightly judge us harshly.
“Time is pressing as football burns through its cash reserves with no sign yet of a resumption of the game.
“We are committed to finishing the professional football season as this resolves the issues of promotion and relegation together with title winners on merit.
“However, we may not be able to finish the season as football is not our priority, human life is, and we will do as the Government directs as the pandemic unfolds.”