The bent bulkhead was brought to the attention of officials after the morning session on the first day of the championships at Moana Pool.
Because of the bulkhead bow, swimmers in the seventh and eighth lanes had to swim between 15mm and 20mm further than those in the middle lanes.
It was significant for the sprints and could prove costly in the distance events. There are 16 laps in the 400m.
Organising committee chairman Michael Dodds made sure the problem was rectified.
"We just have to loosen the lane ropes on both sides of the bulkhead," he said.
The event is swum in a 25m pool, and the bulkhead is put in place to divide the 50m Moana Pool into two parts. The shallow end is used by swimmers in their warm-up and warm-down.
Dunedin City Council aquatic services manager Steve Prescott said International Swimming Federation (Fina) regulations allow for a 2mm tolerance. It was more than this at Moana Pool yesterday.
"If someone tightens the lane ropes too tight, it often hangs in a bow," Prescott said. "It is just a matter of loosening it off and it comes back to normal."
Cliff Threadgold, the coach of Hamilton's Ace Swimming Club, saw the bow when he was watching his swimmers at poolside.
His daughter, Kirsty Threadgold, was at a disadvantage when she swam in lane six in the heats of the 400m freestyle.
"The middle lanes had a significant advantage," he said.
It was Threadgold's first trip to Dunedin for a swimming event and, apart from that one hiccup on the first morning, he was pleased with the facilities at Moana Pool.
"The overall facilities are great," he said. "I'm happy to come to Dunedin instead of always travelling to Auckland or Wellington."
The second-division championships continue for the next three days and end on Saturday evening.
