A report from the Ministry for Primary Industries shows two New Zealand sea lions were killed in the week to Sunday May 14, and another one was killed earlier this year.
They were killed during squid trawling.
The sea lions are one of the rarest species of seal in the world and found only in New Zealand.
Forest and Bird said the deaths of the creatures was not reported by the ministry or the fishing industry at a recent sea lion advisory management meeting that was attended by environmental and mana whenua representatives.
The group said the ministry and industry were collaborating and withheld the information from the meeting knowing it would strengthen calls for tougher regulation.
Forest and Bird marine conservation advocate Katrina Goddard said it was incredibly disappointing they were participating in good faith, while information was being held back.
"The fishing industry is killing this animal and we need some urgent action to stop this."
She said it reinforced the need for more proof that the industry's sea lion exclusion devices that are used in trawl nets - known as SLEDs - actually work.
"We've got so much evidence now that they are killing sea lions and there's no science to back-up that they are working."
In a statement, the ministry said that any death of a sea lion was disappointing.
"However, while regrettable, these captures are consistent with observed capture levels in recent years and do not constitute a threat to the Auckland Islands sea lion population."
The ministry rejected the suggestion it had colluded with industry or anyone else to withhold the information from the Forum and Advisory Group.
It said it shared news of the captures with the group on Friday 19 May, as part of its regular weekly update.
However, Forest and Bird said that the news of the deaths was emailed out on Friday afternoon in its standard report and not raised at the actual meetings which took place in the days prior to that.