The FA says results in those divisions, including the Isthmian South East where Guernsey FC play, will be expunged.
It means the Bulls' perfect record of 27 wins from 27 in Combined Counties Division One will disappear from the record books, with the club forced to start from scratch at the same level next season.
The FA's knockout competitions, including the Inter-League Cup - in which Jersey's representative side have reached the last four - could still be completed, however.
The NLS and the women’s football pyramid were able to build a consensus amongst their leagues and, where possible, aimed to create a consistent approach across all leagues, whilst taking into account the unique characteristics of each individual league. As a result, The FA and NLS steps three to six have reached a consensus that their 2019-20 season will now be brought to an end, and all results will be expunged. This will mean no promotion or relegation of clubs between NLS steps three to six, and no promotion to NLS step two.
Jersey Bulls' committee met on Thursday evening, following the announcement.
In a statement, chairman Russell Le Feuvre said the club were "disappointed" with the decision and that they would be "engaging further" with the FA and Combined Counties Football League.
WATCH this clip with Bulls caption James Querée...