President Carter's chosen appointee to be director of the Arms Control and Disarmament Agency was a member for three months earlier this year of a national organization set up to "stop SALT II" on grounds that the expected strategic arms limitation treaty with the Soviet Union will "lock the U.S. into military inferiority."

This brief affilliation of Army Lt. Gen. George Seignious (Ret.) with the American Security Council's "Coalition for Peace Through Strength" is causing concern among administration officials responsible for sending the arms control nomination to the Senate for confirmation.

According to some official sources, the possibility of controversy arising from the membership in the anti-SALT group may cause the White House to withhold a recess appointment which Seignious has requested to allow him to assume his arms control duties before Congress returns in January. Presidents have been reluctant to make such interim appointments if there is a substantial chance of a battle over confirmation.

Seignious, interviewed by telephone from his office as president of The Citadel, a Charleston, S.C., military academy, yesterday described his membership in the coalition as a result of administrative errors. He said he did not know at the time he joined that the organization opposed the strategic arms limitation treaty.

The 57-year-old retired general, who has served as delegate-at-large on the U.S. strategic arms negotiating team since September 1977, said it is "inconceivable" that he could have knowingly joined an anti-SALT group while serving as one of the negotiators of the pact.

John M. Fisher, president of the American Security Council and a prime mover in the anti-SALT coalition, said Seignious was invited to join the coalition April 26 and accepted by mail on July 7. Fisher maintained that the letter of invitation said that one of the purposes was to "stop SALT II."

Seignious said the original correspondence was lost and that he joined after receiving a follow-up letter listing several former high-ranking military officers as sponsors. However, he maintained that he knew nothing about the group's position on SALT at the time he joined.

Seignious resigned in a letter dated Oct. 17, declaring that as SALT delegate-at-large "I personally resent the distorted and untrue statements" about SALT contained in the group's literature.

The letter was written a few days after a luncheon with presidential assistant Zbigniew Brzezinski at which the directorship of the arms agency was first broached to Seignious, and about the same time as a White House meeting with Carter to discuss the appointment. Conceding that the timing of the letter gives an opposite impression, Seignious said it is "untrue" that anyone in the Carter administration asked him to get out of the anti-SALT organization.

"I think a strategic arms agreement is absolutely in the best interest and the security interest of the United States. If the remaining problems are successfully negotiated, I can and will support it," Seignious said.

Unlike his predecessor, Paul C. Warnke, the former general is not being designated to be chief SALT negotiator as well as arms control agency director. Nevertheless, he is expected to have a key role in selling the treaty to the Senate and administering the agreement if and when it is ratified.

Fisher said he plans to circulate his correspondence with Seignious to the anti-SALT organization's membership, including 175 members of Congress. Fisher said the manner of Seignious "sharp reversal" raises questions about his fitness for a high position that requires "a certain degree of reasonableness."