Manager Gary Croydon says he is "very concerned" about Burgess Hill becoming an Isthmian League club following the restructuring of non-league football.
FA officials were joined by representatives of the Conference, Northern, Isthmian and Southern Leagues on Sunday to finalise the changes.
Crawley take their place in the Conference after winning the Dr Martens premier division title.
Bognor and Eastbourne Borough are included in the new Conference south division after finishing in the top 13 of the Ryman and Dr Martens premier divisions respectively.
They are joined by Lewes who won the Ryman division one south title and three play-off games.
Ryman division one south runners-up Worthing are the only Sussex club to be included in the Isthmian premier division.
Burgess Hill and Hastings have been involved in the biggest shake-up. They switch from the Southern League to the Isthmian (Ryman) League and join Horsham in division one.
It will reduce travelling for both clubs and there is the prospect of a bumper pay-day because well-supported Combined Counties champions AFC Wimbledon are included in the league.
But Croydon is not happy with the switch because of the way Lewes were treated by the Ryman League in the play-offs.
The league attempted to alter the opposition and venue for their final play-off game on Saturday and the FA had to step in and change it back.
Croydon said: "We are very concerned about becoming a Ryman League club after what happened to Lewes.
"It was a fiasco and it was not the first time something like that has involved the Ryman League. They said Lewes could not go up last season because one turnstile didn't work.
"They also took the FA to court about restructuring even though everyone knew nothing would come of it.
"I don't want to get off on the wrong foot with the Ryman League and we will play wherever we are put but I can't stress enough how concerned we are about it.
"We were very proud to be a Southern League club and we would have much preferred to stay in that league.
"They have been well organised and professional, so I look forward to meeting with the Ryman League to find out how things are."
Horsham manager John Maggs has welcomed the changes, even though they have pushed his team further down the non-league pyramid.
Horsham are now three divisions below Conference one.
Maggs said: "I'm delighted with the restructuring. People talk about relegation but when you look at the clubs in our league, there's no way we will be playing at a lower level.
"There are some very strong teams involved. In fact, when you look at the premier division, it is probably just as strong.
"Clubs like AFC Wimbledon, Dulwich and Tooting are going to be challenging and then there's Burgess Hill and Hastings, who I think will both be a force.
"It will make it very hard for us to get out of but I still welcome the changes because it's a challenge and we will be stronger next season."
Maggs believes the introduction of new teams will attract more supporters to Queen Street.
He said: "If I was a supporter, I'd be very excited about the new season. They will have the chance to go to different grounds and see different teams."
Worthing are also looking forward to next season. The Rebels are relishing the prospect of facing former Conference sides such as Kingstonian and Dover. Assistant manager Danny Bloor said: "It's great for us. We want to be playing at a high level of football."
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