The monitoring is designed to curb the practice of high grading, where tonnes of small but legal-sized fish are dumped back into the sea so trawlers can target larger fish.
Recreational fishing lobby group Legasea has welcomed moves to reduce commercial waste.
'It's taken more than 30 years to get recognition of this issue and a plan to address this waste," national programme leader Mandy Kupenga said.
"If Mr Guy's proposed initiatives are implemented thoroughly it will make a significant impact on rebuilding the fish stocks."
However, the decision to leave the commercial size limit at 25cm and leave the commercial quota untouched while adjusting both the size and bag limits for recreational fishers was disappointing, Ms Kupenga said.
Changes to the fishery's management included cutting the recreational bag limit for snapper from nine to seven and raising the minimum size limit from 27cm to 30cm.
An initial suggestion in a ministry discussion paper of cutting the recreational bag limit to three fish created a huge public outcry, with more than 49,000 submissions made on the proposed changes.