The school's first XV, which beat King's High School last Saturday to make the final against Southland Boys' High School, has been told it can not play at Forsyth Barr Stadium, University Oval or Carisbrook.
It may be forced to play at Littlebourne, which has been described as a mudheap, which cut up badly in the semifinal against King's.
It will be the first time Dunedin has hosted the final.
Otago Boys' High School rugby manager Brian Ashwin said he was frantically looking around for a ground, and was disappointed the game could not be played at the new stadium.
He said with a large crowd of up to 3000 expected, he wanted to play at a ground which had a grandstand. It would be too dangerous to play on a ground with no seating as people would struggle to get a view.
University Oval was out as it was being kept clear for World Cup training, while Carisbrook had four games played on it on Saturday and needs a few weeks to recover.
Ashwin said it disappointed him that such a big game could not be allocated a top ground. He was hopeful of getting approval touse University Oval. Tahuna Park was also an option but its facilities were average and it was susceptible to bad weather.
Dunedin Venues Management Ltd David Davies said at any other time he would be more than willing to let the school game be played at Forsyth Barr Stadium.
But there had been some slight damage to the stadium grass by the stage at last Friday's opening and some seeding repairs were required.
"Perhaps I am being over-cautious and I will take that on the chin. But we want to make sure that come the World Cup the ground is absolutely pristine. The eyes of the world will be on us and we just want it to be perfect," Davies said.
"If this was this time next year then I would be more than willing but I just want to protect the ground."
The Otago ITM Cup side would train on the ground this morning, but a training session was different, and the damaged turf would be protected.
Davies said World Cup teams would start training on the ground on September 1 so there was not a lot of time to get everything ready.
The ground would be fine to be used next Wednesday when Otago plays Manawatu in the ITM Cup.