For example, he said, marine reserves in the EEZ would interfere with New Zealand's obligations to allow undersea cables to be constructed within this area.
Dr Smith said no-take zones in the deep seas could still be created through one-off, specialised law changes.
This approach was being used to establish a vast ocean sanctuary around the Kermadec Islands, 1000km northeast of the North Island.
In a discussion document released yesterday, the Ministry for the Environment said that the greatest threats to biodiversity were within the territorial seas. The territorial seas also contained the most competition for resources and access, the largest proportion of fishing activity, and were the most thoroughly-researched.
"As our knowledge of the marine environment in New Zealand's exclusive economic zone and continental shelf increases over time, there may be a case for extending the proposed categories of protection to these areas," the ministry said.
Worldwide Fund for Nature (WWF) New Zealand said it was "dismayed" that the new framework would not cover the EEZ.
Forest and Bird marine advocate Anton van Helden said the narrow focus of the reforms meant there was no formal process to protect 96 per cent of New Zealand's waters. He said a system for creating reserves in the deep seas would have been simpler than close to shore because there were fewer interested parties.
Green Party environment spokeswoman Eugenie Sage said the Government's decision left the EEZ to be "plundered by oil and gas interests".
This was rejected by Dr Smith, who said all deep-sea mining applications had to get Environmental Protection Agency approval.
The main proposal in the reforms is for a broader range of protective measures than just no-take zones, including reserves which target specific species or allow some recreational or commercial fishing.
Consultation on the changes closes on March 11.
PROTECTED WATERS
• 10 per cent of New Zealand's territorial seas (out to 12 miles) covered by marine reserves
• 0.4 per cent of all New Zealand waters (out to 200 miles) covered by marine reserves
• 30 per cent of seabeds and seamounts protected within exclusive economic zone
• New Kermadec Islands sanctuary will mean 15 per cent of exclusive economic zone is protected