The Pars have been ordered to appear before an SFA hearing at Hampden on Thursday, May 9.
And the Fife club - who entered administration earlier this month in a bid to stave off a winding-up order launched by Her Majesty's Revenue and Customs over a £134,000 unpaid tax bill - have until Monday, April 29, to respond to the complaint.
The Scottish Football League have already docked the First Division side 15 points after suffering the insolvency event.
The SFL punishments, which were handed out on April 9, also include a transfer embargo which prohibits the Pars signing players aged over 21 until they come out of administration.
And they will also be subject to a further 10-point penalty and be required to pay a £150,000 guarantee if they do not secure a Company Voluntary Arrangement by the start of next season.
Among the penalties open to the SFA should they find the club guilty of breaking Disciplinary Rule 14 (g) are the termination or suspension of the club's membership or the issuing of a fine.
Rangers were the first club to be punished under rule 14 when it was implemented last year, with the Ibrox club handed a £50,000 fine by the SFA after going into administration in February 2012.
Dunfermline also owe around £8.5 million to former owner Gavin Masterton and other companies. Eight players - including club captain Jordan McMillan - were made redundant by administrator Bryan Jackson after he was brought in to balance the books.