The punishment was delivered by the Rugby Football League's board of directors and sees Halifax, Hull and St Helens all lose two competition points from their 2003 total with immediate effect.
The clubs have 14 days in which to lodge an appeal against the decision.
Said an RFL statement: "Within the salary cap regulations for Tetley’s Super League clubs, the set limits for spending on salaries is no more than 50 per cent of the club’s salary cap relevant income or an upper limit of £1.8m.
"The Rugby Football League will not be making any further comment on any of the three clubs’ positions."
