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The fishery operates between February and May each year and is estimated to be worth about $80 million.
Arrow squid is one of New Zealand's largest and most valuable fish exports.
The fishery will be closed once the maximum number of fishing-related sea lion deaths for the 2009 fishing season reaches 113.
Mr Heatley said the Fisheries Act required him to allow for squid fishing while ensuring the sustainability of the sea lion population.
"I believe my decision meets my dual obligations."
Mr Heatley said he had erred on the side of caution when setting the sea lion limit for the upcoming squid trawl season.
"The latest scientific analysis and the recommendation from the Ministry of Fisheries indicated that the minister could have set the limit as high as 249 sea lions."
The squid fishing industry voluntarily uses sea lion exclusion devices (Sleds), which allow sea lions to escape from trawl nets.
Before the trawlers leave port, the Sleds will be audited to ensure they are installed correctly and are as effective as possible in minimising accidental captures of sea lions.
In addition, Sleds will be regularly checked by MFish observers and fishery officers throughout the season to ensure they are being used correctly.
The Seafood Industry Council said it supported the decision on sea lion by-catch numbers and would continue to work to reduce individual sea lion deaths.