David Wolff expressed disappointment after confirming that the JC MSFL will feature 46 teams for season 2012/13, down two from the previous campaign.
The league has also dropped one division to leave the Premier with 10 teams and 12 in each of the other three divisions.
Five new sides, including Tottenham Chutzpah and Loughton Orient, have joined.
Mr Wolff, who has been chairman of the league for more than 30 years, said: "It's always disappointing to have less teams, but I still think the league is vibrant. We can only hope the numbers will climb in the future.
"I think the larger divisions will lead to healthier competition, although not all clubs were satisfied with the outcome, especially as some teams have climbed two divisions."
Clubs voted against adopting the repeated substitution which was passed by the MJSL last week.
Two new teams - Manchester Maccabi 2nd and FC Cosmos - have joined the Manchester Jewish Soccer League for the forthcoming season, while Leeds-based Hyde Park Rovers have withdrawn their membership.