Zamalek fans are demanding chairman Mortada Mansour quits after the club failed to honour a postponed fixture on Sunday.
The Egypt Football Association (EFA) has awarded the points to Al Makasa, who arrived to play the game.
The EFA has added that it will also deduct three points from Zamalek at the end of the season.
The sanctions mean Zamalek are now in effect 27 points behind league leaders Al Ahly, who have a game in hand.
|Egyptian league standings:|
|1 Al Ahly - 24 played 64 points|
|2 Al Makasa - 24 played 57 points (includes 3 pts awarded for Zamalek's non-arrival)|
|3 Al Masry - 22 played 43 points|
|4 Zamalek - 23 played 40 points (with 3 more points to be deducted)|
|5 Smouha - 22 played 40 points|
|6 El Geish - 23 played 35 points|
Security concerns meant that the game could not be played as originally planned on Saturday, which is Christian holiday in Egypt.
Both teams asked for the match be played in midweek as they felt it was also too soon after two Coptic Christian churches were attacked on 9 April.
However the EFA refused that request and scheduled the game for Sunday.
Zamalek's largest and most passionate supporters group the Ultras White Knights have released a statement on social media demanding Mansour's resignation.
They blame the chairman for the clubs problems and have asked fans, ex-players and everyone from Zamalek to 'save the club from Mansour'.
Fans of the club are disowning the club with one tweet saying "this is now Mansour and his sons' club and no longer Zamalek."
Another fan added "we need who stop this man and save our club."
Former Egypt international Mido, who also played and coached the club, is also concerned at what is happening at Zamalek.
"Fighting and winning is the only way to end your suffering, I can't understand why they wanted to postpone the match," he tweeted.
It is not the first time that Mansour has courted controversy.
In 2015 he withdrew the team from the league over referees before going back on that decision.
He also has a reputation for sacking coaches who fail to impress - none of the last five permanent bosses have lasted more than 17 matches.
Sunday's forfeited match should have been a second game in charge for Portuguese coach Augusto Inacio after losing his first on Monday 2-0 to Enppi.