Coventry City, Luton Town and Cardiff City have been put under transfer embargoes for failing to file their club accounts on time.
In every case, the clubs complied with an extension granted by Companies House for the filing of annual accounts, but that extension had not been made by the EFL in its own rules.
All three clubs have issued statements expressing their confidence that the embargo will be removed and have no impact on transfer activity in the summer window.
In a statement, Coventry City said: "The Government, due to the Coronavirus crisis, allowed companies to extend the deadline to file company accounts by three months and Coventry City chose to take up this option.
"Unfortunately the EFL has decided not to replicate this extension within their own rules, which surprises us as they have amended a number of other rules due to the Coronavirus pandemic.
"This is purely an administrative embargo imposed by the EFL. This has no effect on the day-to-day running of the club or its finances, and will have no effect on planned transfer activity in the upcoming transfer window."
The club say they will be filing their accounts as required by Companies House within three months of the end of February, at which point the transfer embargo from the EFL will be removed.
Coventry City chief executive Dave Boddy said: "It's disappointing that the EFL have chosen to do this.
"The Government has allowed companies to extend the deadline to file accounts and we chose to do this, extending from the end of February to the end of May.
"It's ridiculous that the EFL's regulations on this do not replicate this approach that the Government has taken, especially when they have amended other rules of their during the pandemic.
"The EFL's imposition of this does not have any effect on us, but it is disappointing nonetheless that they have taken this approach to take action against clubs who are simply doing what the Government is allowing us to do."
A Luton Town statement said: "The club's 2019/20 accounts, whilst finalised, have yet to be signed off by our auditors which will be done well before the statutory deadline.
"Given the exceptionally difficult operating environment caused by the pandemic the requirement to continue to play 'behind closed doors', financial forecasts have rightly been scrutinised much more thoroughly and Companies House provided an extension of the statutory filing deadline to June to create sufficient time to complete this additional work accurately. Indeed, the club will publish unqualified accounts before the end of April."
A statement from Cardiff City said: "The club can assure supporters that this is part of an administrative process imposed by the EFL. It has no bearing on the day-to-day running of the club, nor its finances or sustainability. It will not affect us trading in the summer 2021 transfer window."