Chairman Dave Lamont says Otago United struggles to balance its budget but it will be able to compete in the New Zealand Football Championship this summer.
The league has been rocked by news Waikato is to pull out because of a $90,000 shortfall in funding.
Wellington has also said it might have to withdraw. It could mean the NZFC, which kicks off in three weeks, is reduced to two rounds.
Lamont said Otago United had its coach, Terry Phelan, players and sponsors in place but was not looking further ahead than this season.
"It's always a struggle, and that's the same with all sports. There's just not enough dough around," Lamont said.
"We'll get through this year. Then it depends what they do with the league."
Otago United does not have a massive wage bill and relies on a group of key sponsors to keep the franchise afloat.
"We spread our favours widely so we're not overly committed to anyone," Lamont said.
"We've got several sources of money in areas that are historically loyal to us."
It costs $65,000 to enter the league and most teams have a budget of between $300,000 and $400,000 for the season.
The league has been popular with players and attracted more coverage than earlier attempts at national leagues, but the financial stress it places on the franchises - particularly those in the provinces - is starting to tell.
Lamont said it was no fault of New Zealand Football's that the league was starting to show signs of cracking.
"Football's not like rugby. They can't just write a cheque to cover their problems. Like most other sports, if someone gets in trouble, they can't just be rescued by the national body."
He believes there may come a time when the national league reverts to a club-based competition. Player burnout was a concern when the best players were in action all year round, he said.
"You can play all year for one or two seasons but then it starts to hurt. I think there may need to be some rationalisation there."
NZFC teams must register their intent to play in the competition by tomorrow morning.
There is a national board meeting on Thursday night that will determine what form the league will take.
Lamont said Otago United would support whatever decision the league made.
