Livingston have been banned from registering players by the Scottish Professional Football League.
It comes after the club volunteered evidence of undeclared bonus payments.
In a letter to the Scottish FA and the SPFL, the club allege up to £30,500 was paid, without being subject to tax or National Insurance between 2010-11.
The board claim former chief executive Ged Nixon made those payments without the knowledge of other directors but when contacted he declined to comment.
The remaining directors of the Championship side say they welcome an investigation of the actions of Nixon during his tenure as chief executive and director.
Nixon is currently suing Livingston for £311,000 he believes is due to him in loan repayments and when contacted by BBC Scotland on Tuesday declined to comment because of the ongoing legal case.
Livingston also face SFA charges over alleged rule breaches regarding shareholder Neil Rankine's purported links to East Fife and Dumbarton.
Rankine denies the breaches in question but says he will step away from Livingston rather than damage the club.
Livingston are in debt to the tune of about £1.75m and have led a precarious financial existence in their short history, including administration between 2004-2005 and again in 2009 when the current board, including Nixon, saved the club from liquidation, though they were demoted to the Third Division.
The letter sent by Livingston to the governing bodies was dated 31 July 2014 and the SPFL are expected to release a brief statement on the subject later on Tuesday.