The deduction places the Championship side on minus six points, 13 points adrift at the bottom of the league table.
The club's controversial ownership by Dejphon Chansiri has ended, with insolvency firm Begbies Traynor appointed as administrators.
Culture Secretary Lisa Nandy called the situation "an extremely worrying situation" and highlighted the role of the new Independent Football Regulator in preventing similar issues.
Administrators have urged fans to return to Hillsborough and financially support the club, stating that all revenue will directly aid day-to-day operations and the search for a new owner.
