Clubs were told on Thursday that the loan, worth over £100m, would not be paid on Friday as the EFL attempts to “secure a solution” with the Treasury.
The money was due to cover clubs’ outstanding tax bills.
But a clause added would prevent players from being offered improved deals.
The EFL had thought the clause would apply to the governing body as it will be distributing the cash – and would therefore only apply to executives.
But players are regarded as “relevant individuals” in the agreement for the loan, which is due to come from the Treasury’s Covid Corporate Financing Facility (CCFF).
A spokesperson for HM Treasury said: “The CCFF provides short-term loans to big companies that make a material contribution to the UK economy. It currently helps support almost 2.5 million jobs in the UK.
“Companies wishing to take out loans have to agree to certain conditions on dividends and pay restraint, as taxpayers would expect.”
In December, a bail-out package was agreed, in which the Premier League would pay £15m to secure a £200m interest-free loan for Championship clubs, which would be capped at £8.33m per club and has to be repaid by June 2024.
External sources of funding are being sought and EFL sources are confident this will be secured.
However, this has not yet happened and the £100m-plus loan due to come from the CCFF is regarded as vital.
Despite the urgency of the situation, it is thought unlikely clubs would be willing to agree to a loan that prevented them from making incentive payments to their players.
“We are extremely disappointed by the developments at this late stage of our discussions and we will continue to strongly negotiate with HM Treasury to secure a solution that meets the requirements of Championship clubs and is consistent with the parameters other industries are being asked to meet,” said an EFL spokesperson.
“There remains a significant amount of debt – including HMRC – being stored up by Championship clubs, caused simply by the inability to generate normal levels of income due to the circumstances created by the pandemic.
“With the moratorium on Paye liability enforcement coming to an end on the 31 March, this is very much a live issue for our clubs, who throughout Covid have continued to incur significant costs and need to be able to plan with greater certainty without further risk in order to keep their clubs fully operational for the benefit of their local communities.”