Mussels, who are bottom of the Bostik League South Division, were charged by the league at their last meeting and the club has now been found guilty.
The news will come as a blow to Shoreham boss Sammy Donnelly and his squad, who remain bottom but now have just two points and are seven adrift of second-from-bottom Ashford United.
An official Bostik League statement read: "At their last meeting the league board met with chairman of Shoreham FC (Stuart Slaney) following the club being charged with a registration irregularity. The club admitted the charge under Rule 6.4.1 and were therefore dealt with under Rule 6.9 having played an ineligible player.
The board considered the matter sufficiently serious to warrant a fine of £2,000 and although the club lost both matches in which the player appeared, the club were levied six penalty points."
Bostik League chairman Nick Robinson feels it will work as a warning to other teams.
He said: "This is a sad occasion for a club newly-promoted to step four but is a warning to all clubs to ensure that registration forms are completed correctly, and that the person signing as witness has actually seen the player sign the form."
Shoreham have stated they will not be appealing the decision and the points deduction came in to effect yesterday.
Mussels home league clash with third-from-bottom East Grinstead Town (7.45pm) has had added importance.