The ruling comes following an emergency meeting of team chiefs held earlier today.
It had been claimed that clubs going into administration were winning an unfair advantage by becoming immune to creditors.
Stated League chairman Sir Brian Mawhinney: "This is necessary because the Football League is the guardian of competitiveness in our divisions and we can't have clubs who go into administration gaining an advantage.
"It is a fundamentally different approach and there was a healthy debate - but I pay tribute to the clubs for attaching that significance to it."
Clubs which are dealt the points deduction will have maintain the right to appeal to an independent body.
The meeting also agreed the introduction of parachute payments for clubs relegated into Divisions Two and Three while a new structure for the management of the League was also ratified, giving the First Division their own managing director on a three-man executive team answerable to Mawhinney.
