The Carter administration yesterday bluntly rejected criticism of the strategic arms limitation treaty [SALT II] offered last weekly by Senate Minority Leader Howard H. Baker Jr. [R-Tenn.], saying an amendment Baker has demanded "will kill the treaty."

Gen, George M. M. Seignious II, chief of the Arms Control and Disarmament Agency, speaking at a regional state governors' seminar in New York, gave no indication that the administration might be willing to work out a compromise with Baker. He said instead that it would be "fruitless" to try to change the treaty so that it "would give us everything we might want."

Seignious' speech, the first formal administration comment since Baker's news conference Wednesday, did not mention Baker by name, but the issue that Seignious chose to illustrate how the treaty works was precisely the one Baker denounced most forcefully.

That is the question of whether the Soviet Union's fleet of 308 heavy intercontinental nuclear missiles should be reduced by the SALT agreement. The treaty Carter signed last month would permit the Soviets to retain the full fleet, a provision Baker described as a fatal flaw in the pact.

Baker indicated last week that he would be willing to negotiate with Carter over the heavy missile question and other treaty issues, but Seignious yesterday left little room for compromise.

"in this agreement," he said, "you cannot extract a provision you do not like, attempt to gain unilateral advantage through renegotiation, and still expect the complex edifice to remain standing."

Seignious noted that former president Ford and his secretary of state, Henry A. Kissinger, had agreed to exempt the Soviet heavy missiles from the SALT agreement as part of the Vladivostok accords in 1974, Baker endorsed the Ford-Kissinger position at the time.

Seignious joined Baker in deploring the remarks of Soviet Foreign Minister Andrei S. Gromyko. Gromyko ruffled feathers Monday by warning senators not to make changes in the language.

The treaty cannot take effect unless it is approved by two-thirds of the Senate -- 67 senators.

Baker, as majority leader and as an unannounced middle-of-the-road contender for the GOP presidential nomination next year, has been considered an important influence on the moderate Republican senators whose support Carter needs to win approval.

But Baker's harsh assessment of the treaty, and Seignious' hardly concilliatory remarks yesterday, suggest that the senator and the administration might come to a stalemate and that Baker will end up voting against the agreement.

The administration says it thinks it still could win the necessary Senate votes if it can corral all but a handful of the 59 Democratic senators and a dozen or so Republicans.

Seignious' speech also stressed an issue that has provoked some concern among Senate Democrats: this country's ability to make sure that the Soviets don't violate the treaty.

He said the agreement would "acttually enhance the knowledge we have of Soviet strategic forces," in large part because it would stop the Soviets from encoding radio signals about test firings of missiles. CAPTION: Picture, GEORGE M.M. SEIGNIOUS II . . . no compromise indicated