The Sky Blues played Emma Hollingsworth and Carly Davies – both registered as WSL players – in wins over Huddersfield and Nottingham Forest last month.
Rules state that only one WSL player can take the field for a Premier League club at a time.
The points deduction now leave Coventry six points behind Northern Division leaders Sheffield FC with just two games remaining, with the winners progressing to a play-off.
WPL’s Northern and Southern Divisions title winners meet on Sunday, 24 May with the victor of that game promoted to WSL 2.
The FA Women’s Premier League management committee have applied to the Football Association’s chairman of the appeal board to try allow Coventry to appeal the decision before the play-off.
The Sky Blues, who beat Sporting Albion 1-0 on Thursday to retain the County Cup, have lost just two league matches this season, both against Sheffield.
In a statement the club said they were “extremely disappointed with this decision, particularly as we have never intentionally or knowingly broken any rules.”
Full Coventry City Ladies Football Club statement:
“CCLFC has been charged and found to be in breach of FAWPL Rule 8c concerning eligibility of players on two occasions during April 2015, resulting in a 6 point deduction effective from 6 th May 2015. The Club is extremely disappointed with this decision, particularly as we have never intentionally or knowingly broken any rules. We will be taking this matter under advisement and therefore have no further comment to make at this time while we consider our options.”