Doc community relations ranger Jacob Dexter said the birds, which were mostly young, showed no signs of animal attack so their necks would have to have been broken by people.
However, because of reports of sick and dying birds, it could have been that whoever did it may have been "putting the birds out of their misery" rather than killing them maliciously, he said.
The Massey University scientists who did the autopsies said breaking the birds' necks would have been enough to kill them, but they could not say for sure whether their necks had been broken before or after death.
They also could not find any traces of toxins or diseases in the birds' systems and therefore, "the cause of the mass die-off remains to be established" .
Of the six birds sent for autopsy, only one or two were in a condition where satisfactory tissue samples could be taken for testing.
The others were too decomposed but if it was a toxin or disease responsible for the deaths, it would likely have been in the "fresher" bodies, Mr Dexter said.
The birds were found on Grovers Island, a nesting spot near Roxburgh, and reported to Doc last month but, because of the rate of decomposition, it was thought they had died in December or January.
Mr Dexter said, since beginning his investigations last month, he had talked to several people who had seen sick or dying birds in those months.
Even if the person responsible had been acting to end the birds' suffering, their actions could still be punishable under the Wildlife Act, he said.
The Act stated, if convicted, a person faced up to six months' imprisonment, a fine of up to $100,000 as well as an extra fine of up to $5000 for each animal harmed.
Because the deaths had been reported so late, it would be hard to track down who was responsible for the broken necks, unless they came forward, Mr Dexter said.
"It's just a shame that it was reported so late because we know that people saw them in December."
If Doc had been made aware of the state of the birds at that time, it might have been able to save some of them or at least get a better idea of what was affecting them.
Grovers Island is thought to be the only nesting site for black-billed gulls, as well as black-fronted terns, in Central Otago.
Mr Dexter said he had worked in the area for four years and had never heard of this kind of thing happening before, but he would monitor the site.
The birds are listed as nationally endangered, but it was not known how many lived in the colony breeding on that particular island and, therefore, it was not known how significant the 60 deaths were.
Mr Dexter previously estimated the entire black-billed gull population to be in the thousands, but said the population was declining.
The birds were "generally restricted to the lower half of the South Island", he said.
The colony had returned to the coast for winter, as had the colony of black-fronted terns, but he was unaware of any dead birds turning up on the coast.
