Figures from the 2015-16 fishing year show 140 birds were caught on surface longlines on those commercial boats being observed by government monitors.
For that year only 320,000 of the total 2,355,000 hooks were monitored.
When extrapolated out it is estimated more than 800 albatrosses were killed as well as 51 black petrels - a species found to be the most endangered seabird in last week's Parliamentary Commissioner for the Environment's report
It noted under an international agreement New Zealand had "an obligation to conserve albatrosses and petrels" and said the government was considering a proposal to make line-weighting mandatory in an attempt to do that.
Forest & Bird seabird advocate Karen Baird said the government and fishing industry should commit to a zero seabird by-catch goal and do more to protect them.
"We're not making any progress, we haven't got any new regulations in place. Seabirds are still being caught to a very high degree and populations are under threat.
"So our birds are in crisis and MPI [Ministry for Primary Industries] doesn't seem to be doing anything about it."
Ms Baird has sat on the seabird advisory group established in 2013 to look into the effectiveness of the national plan to protest seabirds.
"I've seen very little progress indeed and so I'm pretty unhappy about what's going on."
She said said albatrosses had a tendency to be caught as by-catch because they often followed fishing boats.
"They'll attack baited hooks and become hooked. We just don't have sufficient mitigations in place to prevent that."
The Ministry for Primary Industry has acknowledged 2016 was "a particularly bad year" for seabirds and surface longline fishing.
Spokesperson Dave Turner said MPI recognised the risk to threatened seabird species and was committed to having the most effective mitigation measures.
"MPI has worked with industry in this area for some time and regularly reiterates the importance of bird mitigation and the need to comply with regulations designed to prevent seabird by-catch."