The National Oceanic and Atmospheric Administration's Fisheries Service proposed that the upper Cook Inlet, the middle inlet and a strip along the lower western shore, as well as Kachemak Bay, be designated as critical habitat for belugas.
"Protecting these endangered whales is one of our top priorities," said Doug Mecum, the service's acting administrator for Alaska.
Public meetings will be held before a final rule is issued next year.
Cook Inlet's beluga whales are listed as endangered under the Endangered Species Act. Only 321 of the animals are left, down from an estimated 1,300 in the inlet in the 1980s.
While overharvesting by Alaska Natives was largely responsible for the initial decline, the whales have not recovered despite a decade of nearly no hunting. The population continues to drop by 1.5 percent a year.
The state strongly opposes both the listing and critical habitat designation because of concerns about development.
"Listing more than 3,000 square miles of Cook Inlet as critical habitat would do little to help grow the beluga population, but it would devastate economic opportunities in the region," said Gov. Sean Parnell. The state is reviewing its legal options.
According to NOAA, critical habitat designation would not stop development such as the expansion of the Port of Anchorage, mining, and gas exploration, but it would mean additional review for projects needing federal permits.
The team working on the $700 million port expansion project already has been coordinating with federal agencies on the whale issue, said Suzanne Armstrong, port director of marketing and public affairs. She said 25 permit conditions are attached to the expansion project to mitigate effects on belugas.
Armstrong said the designation is likely to have an impact but the extent remains to be seen. "What we know for sure is not much," she said.