The Supreme Court ruled 6 to 3 yesterday that operation of a nearly complete Tennessee Valley Authority dam must yield to the preservation of a threatened fish species called the snail darter.

The "language, history and structure" of the Endangered Species Act of 1973 demonstrate "beyond doubt that Congress intended endangered species to be afforded the highest of priorities," Chief Justice Warren E. Burger wrote in the opinion for the court.

From the bench, he said that there is "something more important" than either the three-inch fish or the Tellico River land development project, for which Congress has budgeted $120 million - less than one-fifth of it for the dam itself.

"Very fundamental principles of the separation of powers" among the branches of government are at stake, Burger said orally.

Also from the bench, dissenting Justice Lewis F. Powell Jr. said, "Today the fish wins 100 percent."

Burger rejected the argument in Powell's written opinion that the court should view the act "reasonably" and shape a remedy "that accords with some modicum of commonsense and the public weal."

But that is not the court's function, Burger wrote. "Congress has spoken in the plainest of words, making it abundantly clear that the balance has been struck in favor of affording endangered species the highest of priorities. . . In our constitutional system the commitment to the separation of powers is too fundamental for us to pre-empt congressional action by judicially decreeing what accords with 'commonsense and the public weal.'"

In contrast, Powell, joined by Justice Harry A. Blackmun, read "the total record as compelling rejection of the court's conclusion that Congress intended the Endangered Species Act to apply to completed or substantially completed projects such as the dam and reservoir project that today's opinion brings to an end - absent relief by Congress itself."

Seeking that "relief" are Senate Minority Leader Howard H. Baker Jr. (R-Tenn.) and Sen. John C. Culver (D-Iowa), chairman of the resource protection subcommittee. The parent Environment and Public Works Committee has reported their bill to create a seven-member interagency body to decide when a project should take precedence over an endangered species.

The decision "will accelerate the possibilities of passing" the bill in this session, Baker said.

The White House hasn't taken a stand on the bill.

Two of its agencies, the Office of Management and Budget and the Council on Environmental Quality, and the Interior Department, had wanted the Justice Department to side with environmentalists in the Supreme Court.

If TVA should complete the dam, they contended, it would, in violation of the law, inundate the only known habitat of the darter in the Little Tennessee River, as well as 16,500 acres of valuable farmland and native American and Cherokee Indian archeological sites.

But Attorney General Griffin B. Bell, making his debut argument in the Supreme Court, sided with TVA. He urged the justices to reverse a decision by the 6th U.S. Circuit Court of Appeals that completion of the dam would violate the law by causing the disappearance of "a unique form of life."

The chief justice, in his remarks from the bench, recalled that Bell had brought to the lectern a dead darter "encased in a small flask." Bell's apparent purpose was to cast the case in the form of a dam, which is one part of a multipurpose regional project designed mainly to stimulate shoreline development, generate power to heat 20,000 homes, and provide water recreation and flood control.

In other reactions to yesterday's decision:

New TVA board chairman S. David Freeman, who has been critical from the start of the agency's hardline policy of proceeding with the dam, and Interior Secretary Cecil D. Andrus each announced that they will work closely to try to save the darter, to make the best use possible of the $100 million invested up to now in the whole project, and to find alternatives to scrapping it that, Freeman said, "may even produce greater benefits for the people. . ." Freeman and Assistant Interior Secretary Robert L. Herbst plan to meet this morning.

Law Prof. Zgmunt Plater of Wayne State Law School in Detroit, who argued the darter case for environmentalists, said he was "delighted" with the decision "because it makes clear what we've been trying to-show all along: this is not a 'little fish vs. big dam' case. It is a question of whether a federal agency must obey federal law, because if TVA had complied with the law's conflict-resolution procedures back in 1973, we would never have had to go to court in the first place."

Lewis Regenstein, vice president of the Fund for Animals, termed the decision a victory for taxpayers as well as snail darters, characterizing the dam as one of several "environmentally destructive government boondoggles" that "are tremendously inflationary and wasteful. . ."

TVA, a public corporation owned by the government, began work on the Tellico project in 1967. One purpose was to convert the fast-flowing Little Tennessee into a 30-mile-long deep reservoir by building the dam and then closing its gates. Congress appropriated money for the project annually.

The snail darter, a tannish, bottom-dwelling previously unknown species of perch, was discovered by a University of Tennessee ichthyologist in 1973. There are an estimated 10,000 to 15,000 of them. Interior's Fish and Wildlife Service says it may take 10 to 15 years to determine if the darter can survive in another environment.

In the case that made its way to the Supreme Court, a key issue was whether Congress intended to let the unexpected discovery of an endangered species prevent completion of a federal project.

In the dissenting opinion, Justice Powell said legislative history contains "not even a hint" that Congress intended such an "absurd result." He relied in part on the continued congressional appropriations of which "at least $53 million" now will be "waste."

But in the same history, Chief Justice Burger found a "plain intent . . . to halt the trend toward species destruction, whatever the cost." To be sure, Senate and House Appropriations committees said repeatedly that they wanted the project completed. But to let such statements rather than the expressed will of Congress prevail would be to repeal legislation by "implication" and to produce another "absurd result," he said: flouting "the very rules the Congress carefully adopted to avoid this . . ."

Justice WIlliam H. Rehniquist dissented separately.