President Carter announced yesterday that he will nominate former Assistant Defense Secretary Paul C. Warnke to be director of the Arms Control and Disarmament Agency and the United States' special negotiator at the Strategic Arms Limitations Talks (SALT).

Carter also announced that he will name Washington lawyer Clifford L. Alexander Jr. to be Secretary of the Army, Alexander, 43, an unsuccessful candidate for mayor of the District of Columbia, would be the first black to head the Army.

Meanwhile, one of the President's top advisers suggested that Carter may name acting Central Intellegence Agency Director E. Henry Knoche as the permanent head of the agency.

Hamilton Jordan, who is directing the administration's search for high-level appointees, said the elevation of Knoche as permanent director is one option that Carter is considering since the withdrawal under congressional pressure of his first choice for the job, former Kennedy administration White House aide Theodore C. Sorensen.

Carter has "a lot of confidence" in Knoche and will likely take his time, perhaps as much as three or four more weeks, before choosing a new CIA director, Jordan said.

The nomination of Warnke could be as controversial as Sorensen's who withdrew his name from consideration after the administration encountered heavy opposition to him on the Senate Intelligence Committee.

Warnke's nomination has already drawn fire from some members of the Senate Armed Service Committee who are expected to question him closely about past remarks he has made about the limited influence of nuclear weapons.

Assistant Senate Majority Leader Alan Craston (D-Calif) said he has urged Jordan and Secretary of State Cyrus R. Vance in separate phone calls to hurry the nomination of Warnke. Cranston said he saw a "substantial majority" for Warnke in the Senate Foreign Relations Committe but a minority base of support in the Senate Armed Services Committee.

Foreign Relations is the committee responsible for conducting the confirmation hearings and making a recommendation to the Senate. But a several Armed Services Committee members, including Sam Nunn (D-Ga.) and Henry M. Jackson (D-Wash.), have called for separate hearings on the nomination. Such a hearing could provide an influential forum for opposition to Warnke.

Warnke, 57, served as the Defense Department's general counsel and from 1967 to 1969 as assistant secretary of defense for international affairs. He is now a senior partner in the Washington law firm headed by former Defense Secretary Clark Clifford.

Alhough he was not discussing the Warnke nomination specifically, Jordan told a breakfast meeting of reporters that Carter's failure to secure Sorensen's nomination in the face of opposition should not be interpreted as a sign that the President will back down on future appointments.

Insisting that Carter was prepared to fight for the Sorensen nomination until Sorensen decided to give up, Jordan said:

"When a President is not willing to fight, he should withdraw the nomination.We were ready to fight. People who think he shies away from a fight or a confrontation are misreading him."

Despite the experience with Sorensen, Jordan said Carter will not poll Senate committee members before making future controversial appointments. To do so, he said, "would be a sign of weakness."

Jordan said "most decisions" on sub-Cabinet appointments have been made but that many of the announcements have been delayed for background checks by the FBI and other agencies.

He also said that it may be "several months" before a successor to FBI Director Clarence M. Kelly is selected by Attorney General Griffin B. Bell