The Ministry of Fisheries says the amount of bladder kelp cleared for harvest under fishing quota management system is modest.
The coastal seaweed is used commercially in natural remedies and as food for humans and is being trialled as animal feed.
The ministry's chief executive, Wayne McNee, says catch limits have been limited to just over 1200 tonnes from a small area near Banks Peninsula and about 300 tonnes from the Chatham Islands.
Mr McNee says the quota is modest, considering the vast amounts of kelp that grow on the South Island's east coast.
He says the ministry is aware the kelp has an important place in the ecosystem and the effect the harvest has on other species will be monitored.
The bladder kelp can be harvested for the first time from October.