The Peter Morrison Trophy will revert to its original format for season 2016/17, the National Maccabi Football Committee have confirmed.
There were mixed feelings about the decision to make the competition, nicknamed The Jewish FA Cup, national from the first round.
Organisers were criticised by some clubs, while several London teams forfeited ties in the early rounds against teams from the provinces and MJSL.
Hendon United Sports Club A won the trophy for the third consecutive season in May, beating double winners North London Raiders in the final at Wingate & Finchley.
The National Maccabi Football Committee recently held its AGM where it was decided that the competition will operate on a 'regional basis until the last 16. The final 16 teams will consist of 12 from the Southern Zone and four from the North.
Commenting the decision, an Oakwood spokesman told JC Sport: "We're always very happy to travel and hope to do so again. It's a shame others aren't."
A representative from South Manchester Sports Club told JC Sport: "It's a shame the format has to be changed to suit those who are unwilling to travel."
South Manchester chairman Jonny Davis voiced his concerns and described the NMFC as weak.
"The Peter Morrison is a National Football Competition, teams who enter know the rules, they also know they may have to travel to the north of England," Davis told JC Sport. "It's quite simple if you don’t want to travel, don`t enter the competition.
"Last season South Manchester, Manchester Maccabi and AFC Flixton were all drawn to play in London, all matches were played without any fuss, however teams from the south could not be bothered to travel.
"A weak organising committee does not help; you either have a national competition or you keep mollycoddling your southern teams.
"The southern teams who do travel are not included in this attack. It is also quite incredible that the northern representative was not even told about the changes.
"It is a very sad state of affairs when certain clubs seem to run the competition. Very sad day in amateur football."