A net positioned off St Kilda beach in late December had three holes big enough to swim through, say free divers Nick Holmes and Chris Garden.
Mr Holmes told the Otago Daily Times the net with the holes had remained in place for up to a month and he had made repeated visits to study the net's condition.
The pair took photographs swimming through the holes before reporting their concerns to the council, he said.
Council parks and reserves team leader Martin Thompson yesterday confirmed a complaint had been received late last year.
However, fresh questions would be asked of the contractor tasked with maintaining the nets following Mr Holmes' claims the damaged nets remained in the water for a month, he said.
"We would expect the contractor to pick that up earlier," he said.
"We will check with the contractor to make sure that has been done."
The contractor, commercial fisherman Graeme Fraser, said when contacted he had been fulfilling the terms of his contract, including replacing three nets in the past two months but could not recall any with three holes in them.
"I don't believe that," he said.
He said checks involved pulling the shark nets from the water and on to a net roller to be checked on board his ship. If holes were found, a fresh net was set and the damaged one taken on shore for repairs.
"I don't know what this guy is on about. That's what the contract states - the nets are repaired and we get new nets made."
Mr Fraser said he had not yet been contacted by the council.
Mr Thompson said the council budgeted $36,200 each year to maintain three pairs of 100m-long nets protecting St Clair, St Kilda and Brighton beaches during the summer months.
The budget paid for the contractor to check the nets twice weekly and make repairs, and that covered the $1500 cost of purchasing one new net each year, he said.
The existing nets had a lifespan of about five years.
It was "not uncommon" for tears in the nets to appear as a result of tidal movements, storms, driftwood and other objects in the water, or even during a shark capture, he said.
However, it was unlikely the holes had put the public at greater risk of shark attack, given the nets did not cover the length of the protected beaches and sharks could "go around them" anyway, he said.
It was a point made during debates about scrapping the budget for the nets in 2004, when community and recreation services manager Mick Reece said they provided only a "placebo effect" for swimmers.
Cr Neil Collins argued against the move, saying "saving lives is more important than saving money", and the nets were eventually spared.
Yesterday, Mr Thompson said there had been no further talk of scrapping the nets since 2007.
They were credited with catching 676 mainly smaller sharks - including sevengill, thresher and tope sharks - since records began in 1977.
The tally included 11 sharks caught in nets at the three beaches in December, as well as a further 10 last month, he said.
