Two died while a third was euthanised, after being shot at the Waitaki River mouth, north of Ōamaru, on Saturday.
Police and the Department of Conservation (Doc) are investigating.
The Otago Daily Times has chosen not to publish Doc-supplied photos of the dead sea lions, owing to their graphic nature.
Sea Lion Trust co-chair Shaun McConkey said he found the shootings unfathomable.
"I personally can't understand it. It seems crazy to me," McConkey said.
"The only defence that we've heard from any members of the public is over concern that the sea lions are stealing their fish - somehow."It followed the death of three sea lions in the Catlins last year.
Doc operations director for the South Island Aaron Fleming told RNZ there had been a disturbing trend of attacks on sea lions.
"We shouldn't have these acts happening across the country, it really does have to stop....It is not only heartless, it is also illegal. And there are consequences for people who are found to be reckless in this way."
There were only about 10,000 New Zealand sealions remaining, Fleming said.
He said it was "completely horrifying and simply not good enough".
"As a country we pride ourselves on our native wildlife and these acts are not who we are. Our precious taonga deserve much better.
Most people are rightly appalled when they hear of these cowardly acts so we are hopeful that someone, somewhere will have a conscience and come forward and tell us what they know.”
pup and her mother were found dead with gunshot wounds in September and October while a third female was found with stab wounds in November and had to be euthanised.
A $50,000 reward was offered for information leading to a conviction in relation to those deaths.
But McConkey, who was calling for Oceans and Fisheries Minister Shane Jones to publicly condemn the killings, said he hoped money would not be needed to motivate those with information.
"We've certainly got plenty of people saying how disgusted and and heartbroken they are by this sort of attitude and it certainly doesn't seem to be a common one. It's much more common for people to be appalled by this sort of act. So we're hoping that just that sense of disgust is going to be enough to bring people forward and and hopefully catch the perpetrators."
Sea lions had not long returned to parts of the South Island's coast, which made the recent killings all the more shocking, McConkey said.
"To me it would be like if kiwi started returning to the forest around Wellington and people went out and shot them - to me that's a similar sort of situation," he said.
Police want the public's help to identify those responsible for the latest shootings.
Anyone with information should contact Doc on 0800 DOC HOT, the police on 105 or at the Oamaru police station.
- additional reporting Allied Media
