Wigan Athletic administrator Gerald Krasner has said the club have appealed against their 12-point deduction.
The English Football League (EFL) said the punishment - for being put into administration - would apply this season if Wigan finish outside the bottom three in the Championship.
"The only grounds we have is 'force majeure'," said Krasner. "This situation was totally unexpected, so we believe this case applies."
The EFL will also investigate how the Latics have ended up in administration.
Force majeure events are usually defined as certain acts, events or circumstances beyond the control of the involved parties, such as natural disasters, war or a pandemic.
In addition, Wigan are facing a further points deduction of up to 15 points should any new owner fail to pay 25% of the money owed to non-football creditors.
In a statement, the EFL said it "acknowledges it is a difficult time for any club placed into administration, particularly in the midst of Covid-19, but is mindful that its regulations are to be applied consistently and equally to all member clubs irrespective of the circumstances".
Wigan staff made redundant
Krasner confirmed 75 support staff were made redundant on Monday and that senior club executives have agreed to work for nothing until the situation is resolved.
He also said all furloughed staff were being paid in full on Tuesday, with the first-team squad getting 20% of their salaries.
BBC Sport understands the staff being laid off include some who work with manager Paul Cook on the recruitment side of the club.
Krasner also said he was "very confident" the club would be able to finish the season, but added: "I'm slightly less confident but still optimistic that we'll get a sale through. It's early days but it's going in the right direction."
Krasner has sent out 50 non-disclosure agreements and final offers for the club should be made by 21 July.
"From that 50 people, three have sent it back with proof of funds, so we're over the first hurdle, nine to go as they say," he added.
"I think we may whittle the 50 down to two or three, but we only need the one buyer."
What do the owners say?
The Latics were placed in administration on 1 July, just weeks after the club changed Hong Kong-based owners.
In a statement, businessman Au Yeung Wai Kay, who heads Wigan's owners Next Leader Fund, said he has "invested more than £40m" in the club and blamed the coronavirus pandemic for the decision to put it into administration.
"Wigan Athletic is a wonderful football club with rich history and a passionate fanbase," the statement said.
"We bought Wigan Athletic with the best intentions: to create a team that would get the club back into the Premier League.
"Unfortunately, the Covid-19 crisis has severely impacted people and businesses around the world - and Championship football clubs, which rely on fans coming through the turnstiles, are no exception.
"This has fundamentally undermined our ability to fund Wigan Athletic and, after struggling to find a solution, in the end took the difficult decision to put the club into administration to ensure its survival.
"The administrators are now doing everything they can to find a new owner who will secure the future of Wigan Athletic for the sake of the many thousands of devoted Latics fans, and the local community."
Wigan are due to play QPR at the DW Stadium on Wednesday knowing their Championship future is now under severe threat.
A 12-point penalty would send them to the bottom of the table. Wigan, who are 16th, are six points above the relegation zone with five games to play.
In response, the EFL said it "fundamentally disagrees" with Wai's comments about the Covid-19 pandemic undermining the ability to fund the club.
"Whilst it is clear that Covid-19 has undoubtedly presented significant financial challenges to the professional game, evidence of the required source and sufficiency of funding to be invested in or otherwise made available to the club, was provided as part of the recent change of control process," the EFL said.
The EFL acknowledged that there is "significant" anger and frustration among everyone connected to Wigan Athletic.
It says it will assist the club in exiting administration at the earliest opportunity, while discussions are ongoing about the "sale of the club, player transfers and funding required to complete the 2019-20 season".
"We will also engage with the appropriate supporter groups, local politicians and other key stakeholders as appropriate to assist in helping achieve a long-term stable future for the club and its local community," the EFL added.
However, the governing body admits there are "a number of important unanswered questions that require urgent attention" and it welcomes an investigation launched by the administrators to determine why the club have entered administration.