Wednesday are in dispute with the EFL over the sale of their Hillsborough stadium and face sanctions, including a possible points deduction.
The club recently claimed the action was “unlawful”, while the EFL insisted it has sufficient evidence to lay the charge.
The Owls have announced they will continue their fight against the charge after claiming the EFL had refused “to agree a sensible procedure”.
“The club has issued its claim against the EFL for acting unlawfully in relation to its alleged disciplinary charges,” Wednesday said in a statement.
“We have sought to engage with the EFL in order to agree a sensible procedure to resolve the dispute arising from the fact that the club relied upon representations from the EFL in relation to the sale transaction which is the subject of the charges.
“The club regrets that the EFL has so far refused to agree to the club being permitted to make its claim, and refused to agree to a sensible procedure for dealing with the dispute.
“The club will continue to take such steps as it considers necessary to protect and enforce its rights against the EFL and to protect it from unlawful action by the EFL affecting the club and the performance of its team.
“The club will not make any further comment at this stage.”
Wednesday have denied all allegations put forward by the EFL after it opened an investigation into the club’s profitability and sustainability submission for 2017-18.
The Owls have been reported to have registered a £38million profit from the sale of the stadium to a company owned by their chairman Dejphon Chansiri in the wrong year in order to avoid breaching financial fair play rules.
The EFL had said previously the charges would be considered by an independent disciplinary commission with sanctions possibly including a severe points deduction.
Earlier this month, the EFL said it had sufficient evidence to support the misconduct charge.
An EFL spokesman said: “As a result of the disciplinary proceedings announced last month, it would clearly be inappropriate to provide specific comment on matters linked to our comprehensive investigation other than to reiterate that, following the review of a large number of documents provided by the club - some of those seen for the first time - evidence came to light to justify multiple charges of misconduct.”