Six League One clubs have told Sky Sports News they are not confident they can survive the season without fans attending games or a financial bailout.
The coronavirus pandemic has had a huge impact on the league, with some clubs' revenues being down 50 per cent.
There are ongoing discussions between the Premier League, the government and the EFL as to whether financial assistance will be granted.
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15 League One clubs responded to a Sky Sports News survey and 86 per cent of those said they were worried about their current financial situation, while none felt the government were doing enough to get fans back into stadiums.
"My worries, apart from the individual clubs, centre around the pyramid itself," Portsmouth chief executive Mark Catlin told Sky Sports News.
"What is the landscape going to look like, not just for the football pyramid, but for their local communities? I think we are in danger of a complete reshaping of the football structure if we are not careful and address this situation urgently and now.
"The Premier League and the Government have got to stop playing Punch and Judy with each other. This is something that is serious, it is happening now and they need to address it now between them."
It was hoped that fans would be back in stadiums by the start of October, but plans were put on hold as coronavirus cases across the UK started to rise.
Ticket money is crucial to lower league clubs and with their main outgoing being players' wages, many are now reliant on their owners to foot the bill and keep them afloat.
Some clubs feel the government has supported other industries and that football has been left to its own devices, because there is a perception that the entire pyramid is wealthy enough to stand on its own two feet. However, League One and Two clubs are struggling.
"I am concerned that the entire pyramid of professional football in the UK is now completely at risk," Rochdale chief executive David Bottomley told Sky Sports News.
"The parties involved, the Government, PFA and the EFL need to work together now if the professional game is to survive outside the top two tiers".
100 per cent of surveyed clubs felt the Premier League should offer financial support, whilst 73 per cent felt money should come from the government.
The pandemic has had a massive impact on the sporting world and the Premier League is not exempt from that. They suffered £700m worth of losses last season, due to play being delayed.
Whilst they are in talks with the EFL about possible financial support, they already give more in solidarity with the footballing pyramid than any other league in the world.
For many, lower league clubs are the life blood of their towns and cities, as they give back to their local communities. For example, during the pandemic, some opened up facilities for testing centres and antenatal clinics, whilst others helped deliver meals to the vulnerable.
The worry is that without financial support, some clubs will not survive the season, which would have a significant impact on the eco-system of English football and the mental health of so many that work in it.
The government acknowledges that sports clubs are the beating heart of communities and that if some were lost, much more would be lost than just sport. They say getting fans back into stadiums is a priority, as soon as it is safe to do so.