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Southern Counties East League chairman Denise Richmond has expressed her disappointment that they will run with just 19 teams next season.
After Woodstock Sports folded and Lingfield's request to drop to step 6 was granted, only AFC Croydon will replace them for the 2015/16 campaign.
Kent Invicta League title winners Hollands & Blair are also in the 19-team league, with champions Phoenix Sports moving up to Ryman League Division 1 North.
The drop in numbers comes just a year after FA officials mandated that step 5 leagues will run with a minimum of 20 teams per season, which saw Crowborough, Croydon and Lingfield moved across 12 months ago.
"I'm extremely disappointed that we will run one team short of the ideal for step 5 after only one season at 20," said Ms Richmond.
"Following last year's mandate from the FA that all leagues should run with a minimum of 20, it's hard to accept that it's failed at the first hurdle.
"Accepting that clubs have to and should do what is best for them, it highlights how unstable the base of the National League System (NLS) has become after the restructures and reorganisations at steps 1-4.
"Many clubs have been elevated over the last 10 years - some have successfully made the transition, but for some it has been a step too far.
"We hoped that last year would see step 5 football in the region move from strength to strength, but that doesn't seem to be the case."
Ms Richmond was also disappointed that three potential applicants for Kent Invicta League had their hopes dashed by the FA.
FC Elmstead and Forest Hill Park have appealed the decision while AC London were also told they would not be invited to join the pyramid system at step 6.
"The Kent Invicta League received up to 14 applications for membership next season, and following stringent due diligence, endorsed three to the FA," said Ms Richmond, who is the league's chairman.
"All three were rejected by the FA despite the NLS regulations allowing for entry at step 6 after all promotion and relegation issues had been resolved.
"Reasons being given were that they did not receive the support of their existing league, nor their parent FA.
"It's a sad state of affairs when such progressive clubs are blocked. The formation of the Kent Invicta League proves what can be achieved when you step outside of the norm, it's such a shame that others aren't learning from that."