The Interior Department will recommend that the United States disreguard the International Whaling Commission's ban on the killing of the giant bowhead whale, Interior officials said yesterday.

The department's decision to recommend that the State Department file an official objection to the zero bowhead quota places the agency at loggerheads with the Commerce Department and virtually the entire environmental community.

The final decision will probably have to be made by President Carter, after the State Department takes a position next week. The deadline for filing an objections is Oct. 24.

The bowhead issue has become one of the most controversial and emotional of environmental and diplomatic issues since the International Whaling Commission declared last June that the animal was ii danger of extiniction.

Alakan Eskimos, the only hunters of the bowheads say the bowhead hunt is essential to their diet and culture. However, partly as a result of a massive publicity campaign by environmental groups, the State Department has received about 30,000 letters supporting the commission's ban.

Environmentalists and Commerce Department officials who have jurisdiction over marine mammals, argue that the United States, which has taken a strong moral position against whale hunting in the international commission, will lose all credibility if it objects to a ban on killing the bowhead.

However, Interior Under Secretary James Joseph said yesterday, "We reluctantly concluded that the most constructive position is to immediately object to the ban and at the same time come forth with an effective self-regulating program for reducing the take (of bowheads).

"We make this decision reluctantly," he added, "because of our concern to maintain credibility in the international conservation community. However, we are also concerned about our responsibility to our indigenous population groups."

Joseph said a ban on killing as required by the international commission, would be unenforceable because the Eskimos won't cooperate. Instead of a total ban, the department will recommend ways to reduce the killing, hopefully to 10 or 15 year, he said.

Eskimos last year harvested 48 bowheads - an unacceptably high level, according to whale scientists. The eskimos, who hunt with high-powered rifles and explosive harpoons, also reportedly struck 79 other bowheads which escaped but possibly died from their wounds.

Interior Secretary Cecil D. Andrus said he and Joseph "agonized" over the bowhead decision. "You're damned if you do and you're damned if you don't," he said.

"If we come on the side of an objection, then the Russians and the Japanese can say to us - 'Ah ha, you've been kicking us around for years, boys, about how we're wiping out all the resources of the sea, and yet when the sea becomes a little tight on you, you roll over and play dead.' That bothers me. My gut reaction is to come down on the side of the whales.

"But I ask the scientific community how many bowheads are there and they say somewhere between 600 and 2,000. It makes a hell of a lot of difference whether it is 600 or 2,000 - questions they can't answer," Andrus said.

I know full well the Eskimos are going to hunt whales next spring no matter what I say. So then do I ask for the Coast Guard or the Marines to go up there? . . . How are going to fly beef cattle up there for nutrition?

The Eskimo says, 'Nutrition hell - you've just robbed me of my manhood.' I've got a problem . . . I've got to face my trust responsiblities (to the Eskimos)."

The issue has caused a deep split among environmentalists, with Friends of the Earth defending the eskimos and other major national groups including the National Wildlife Federation and Defenders of Wildlife, favoring a total ban on bowhead killing.

"The U.S. has taken the leadership role in the world vis a vis the protection of whales," said William Aron, a Commerce Department oceanographer who heads the U.S. delegation to the International Whaling Commission.

"We have been severely critized by other nations who say we're very tough when it comes to resources that don't affect us. The Russians and the Japanese have had to lay off thousands of workers because the commission reduced the whale quotas.

"Now many people are concerned that if the U.S. does not accept the commission's 16-to-0 vote on the bowhead, our credibility as conservationists will be jeopardized and gains in protection whales will be lost."

Assistant Secretary of State Patsy Mink is reported to favor an objection to the bowhead hunting ban, but a final decision must be made by Secretary Cyrus R. Vance with the concurence of the Commerce Department. Commerce is known to be against an objection, and meetings have already began at the White House to try to resolve the issue.