The National League confirmed it does not intend to resume the 2019-20 season for its three divisions and wants to bring it to a close “as soon as possible”.
It has asked the Football Association to help them with the process and advise how best to decide promotion and relegation issues.
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Thompson says the survival of the clubs, who are facing a financial crisis in the wake of the pandemic, could depend on the league stopping.
“The majority of clubs wanted certainty and with the current lockdown it is very difficult to have a season resume,” he told the PA news agency.
“It allows us, in my opinion and this is just my opinion, to start planning for when we get out of this and when football is going to be important and ready for next season.
“What this measure does is help clubs preserve and consolidate their own clubs to ensure everybody can get through this.
“That is why clubs wanted the season to end so they can start looking at how they can make certain they are more resilient for the new season when it starts.”
The implications of cancelling the season will be felt most by those chasing promotion to the Football League, with Barrow boss Ian Evatt saying the club would not recover if they were to miss out.
But Thompson says such issues are for another day and that there are more pressing issues to resolve.
“We couldn’t even start discussing it until we know what the EFL are doing,” he added.
“But how that might be done would be open to a lot of debate.
“I haven’t really got a view on that one way or the other, I am more concerned about getting our clubs through to the other end. What league or division can be decided by others at a later date.
“My biggest concern, my number one concern, is that clubs can continue paying wages where required and ensure they get through this in one piece.”
Some clubs are already struggling, with Barnet making redundancies last week while Hartlepool have asked staff to take a 20 per cent pay cut.
Thompson is concerned that clubs may not be eligible for the government’s job retention scheme, where 80 per cent of salaries will be covered by the state.
There are some issues around it and the FA is handling it on the clubs’ behalf.
“We are just trying to work out how that fits in with us,” Thompson added. “There are rules around it and it is making certain we can.
“When it was announced on Friday night, a lot of clubs breathed a collective sigh of relief that it was going to help them get through.
“But the detail means it might not be as easy as we first thought and if we don’t get that support I really do fear for clubs.
“It is essential the job retention scheme works for our players. Players at our level are on the normal national wage, they are not on mega money.
“Most of our players earn the equivalent of an average London salary.”
Hartlepool have been hit hard and chief executive Mark Maguire confirmed chairman Raj Singh is continuing to provide financial support, but admitted that more jobs could be lost at Victoria Park as the club attempts to cope with a difficult situation.
In a statement on Pools’ official website, Maguire said: “As such over the last few days, we have made some difficult decisions which have included asking all staff and players to take a 20 per cent reduction in March wages.
“In addition, we have unfortunately terminated the contracts of a small number of members of staff and put the jobs of an additional few at risk of redundancy.
“These actions were taken with a heavy heart and involve individuals who have shown loyal service to the club in some cases over a significant period of time, but these are tough times and we simply must make sure that the club emerges with a sustainable cost base while still being competitive on the pitch.
“(Manager) Dave Challinor has been kept fully up to date with developments and is desperate to get back to work and continue the progress made over the last few months.”
The National League issued a statement to its member clubs informing them of their decision to cancel.
It read: “As many of you will know, the National League held a board discussion yesterday (Monday), which was the third such meeting in 11 days.
“The broad consensus was that our clubs wish for a decision to be made to close the season as soon as possible.
“The National League attended a further meeting last night (by video conference) with the Football Association, and the FA have been asked to assist us with making the decisions to officially postpone all remaining National League fixtures and to end the season as soon as possible for the purposes of player contracts.
“The National League is also working with the FA to define all reasonable and practical options for the determination of the 2019-20 season, and to provide guidance to clubs on dealing with player contracts, player registrations and the application of the Coronavirus Job Retention Scheme.
“We will continue to press for updates and will ensure that any further information is relayed to clubs as soon as it is received.
“The League is very aware that clubs are looking for answers and greater certainty, and we remain focused on delivering these in the most timely manner possible.
“Please keep the flow of information going with the League’s directors and staff, and be assured that we will respond as soon as we can when updates are available on the various issues.”