Etoile are believed to be unhappy over the recent appointment of their former chairman Johan Gouttefangeas as the deputy chief executive officer of the S.League.
Allegations of unpaid bonuses, late payments of salaries, and an unfulfilled promise of a clubhouse dogged the 34-year-old Frenchman's reign at Etoile which came to a sensational end in June last year.
With the new top-flight season in Singapore scheduled to start on February 9, it is believed that these issues coupled with other, as yet unspecified, financial concerns, have prompted Etoile's withdrawal despite prolonged talks with new S.League CEO Lim Chin.
Earlier this week, Mr Lim had gone on record to say that he was confident of a resolution to the Etoile saga, stating that next Tuesday's S.League fixtures draw would feature the 2010 S.League title winners.
The Football Association of Singapore hierarchy will meet on Friday in an attempt to convince Etoile to reconsider, although ESPNSTAR.com understands that plans are already in place for the new domestic season to operate with 13 instead of 14 teams.