The Commerce Department's National Oceanic and Atmospheric Administration is working on two plans that eventually could end the controversial "harvesting" of 25,000 Northern fur seals on the Pribilof Islands, 800 miles southwest of Alaska.

NOAA pays for and supervises the annual harvest by hiring island natives to club bachelor seals to death. NOAA's involvement is particularly irritating to animal protection groups, especially since the harvest is expected to cost taxpayers $500,000 this year.

But it's not easy to end the harvest because "it involved much more than seals," said Richard Roe, director of NOAA's Office of Marine Mammals and Endangered Species.

The 650 natives on the islands are descendants of Russian Aleuts, who settled there centuries ago to harvest seals, Roe said.

When the United States acquired Alaska, it also got the islands. And for reasons that only bureaucrats can explain, Roe's office has ended up administering the islands and looking after the natives.

The Commerce Department spends $5 million a year to support the natives, Roe said, because the only work there is the annual, unprofitable seal harvest.

The Reagan administration is trying to change that by urging Alaska to take over control of the islands and by encouraging the natives to develop a fishing industry.

But both plans are "a long way off," a spokesman said, and the harvests probably will continue for several years.

In the meantime, NOAA will launch this year's harvest on July 6, amid protests from animal groups.

"This is not something that we are proud of," Roe explained, "but it is very complicated."