The White House will nominate retired Army Lt. Gen. Edward L. Rowny as chief U.S. negotiator for any future strategic arms limitation talks (SALT) with the Soviet Union, but there was apparent confusion yesterday about Rowny's independence in the important job.

Rowny, sources say, apparently believes that he should be working for the secretary of state rather than the director of the U.S. Arms Control and Disarmament Agency, as has normally been the case, and that he should have equal rank with the ACDA director and equal access to the president on SALT matters.

Senior administration officials, however, said yesterday that ACDA will continue to carry out basic U.S. arms control strategy, that Rowny will report to the president through the ACDA director and that the ACDA job will continue to rank higher than that of the SALT negotiator.

At the same time yesterday, Sen. Charles Percy (R-Ill.), chairman of the Senate Foreign Relations Committee, said he strongly opposes removing the SALT negotiator's job from the arms control agency. Doing so, he said, "would lead to trouble."

Percy said he had made it clear in a meeting Tuesday with key White House aides and several senate leaders that it is "imperative that the chief chief SALT negotiator work under the direction of, and report through, the director of ACDA."

Percy said he also read to the group sections of the law covering ACDA and assigning principal responsibility for preparation and conduct of negotiations to the agency. Percy said that because no negotiation is more important than SALT, it must not be taken from ACDA.

Percy also said he pointed out a specific section of the law in which "congress expressly intended that the top SALT negotiator be an ACDA executive." When the meeting broke up, Percy added, no objections were voiced to what he had said.

The controversy arose yesterday after The Washington Star reported that Rowny would get the nomination but that he and future ACDA chief Eugene V. Rostow would have equal access to the president.

It was also reported that Rowny would get the nomination but that he and future ACDA chief Eugene V. Rostow would have equal access to the president.

It was also reported that Rowny agreed to the appointment "only after he was promised by the White House that any future SALT negotiations would be outside the purview of ACDA."

Although White House officials say that will not be the case, and Percy seems determined that it will not be the case, Rowny apparently was told something because sources close to him, who asked not to be identified, say he still sees his role as different from that of most previous SALT negotiators.

During the 12-year history of SALT, all but one negotiator, former ambassador U. Alexis Johnson in 1973, was either ACDA director or part of that agency's top level.

Since 1973, the section Percy specifically cited has been added to legislation, and congressional sources say it was intended to prevent the Johnson situation from arising again.

A dose of politics may also be mixed into the bureaucratic confusion and suggestion that Rowny have a bigger role as SALT negotiator.

Rowny represented the Joint Chiefs of Staff on the U.S. SALT team for six years, retiring from the post and the Army in 1979 and making clear he disagreed with portions of the SALT II accord worked out by the Carter administration.

Rowny had been backed for the ACDA job by important Republicans, such as Sen. Jesse Helms (N.C.) and Senate Majority Leader Howard H. Baker Jr. (Tenn.), and was considered a shoo-in for the job.

Sometime during the early months of the Reagan administration, Rowny dropped from contention, and Rostow was picked by the White House for the ACDA job.