Agency officials say noise from the ships in the area might divert or disturb some animals, but not enough to qualify as legal definition of a "take" or harassment.
The drilling area is home to the bowhead, gray and beluga whales, as well as the endangered ringed seal, spotted seal, ribbon seal, bearded seal and harbor porpoise.
Conservation groups and some local Alaskan native groups are fighting the Shell plan. They worry drilling will affect tribal hunting of the bowhead whale, and that any spill would be nearly impossible to clean up because of extreme weather, even during the Arctic summer when the water is free of ice.
"Maybe one well isn't such a big problem, but we really lack is an understanding of what the overall development will look like," said Henry Huntington, science director of the Pew Environment Trust's Arctic program. "NMFS may be right in looking at a narrow case of one summer's exploration wells, but what comes next?"
He noted that a report earlier this year by the U.S. Geological Survey found gaps in the science of how to measure the effects of the underwater noise from oil drilling on marine mammals that use acoustic signals to communicate with each other and find their prey.