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.
