President Reagan declined to say yesterday that Richard V. Allen will get his national security adviser's job back even if he is cleared of all wrongdoing by the Justice Department, and a senior White House official said Deputy Secretary of State William P. Clark now appears the most likely choice for the job.

Reagan said in a press conference that the role of his national security adviser and staff is being reviewed, along with other agencies, to eliminate bottlenecks and make the system work better.

The president seemed to be saying that among the matters under review was whether the role of the national security adviser should remain subordinate to presidential counselor Edwin Meese III. But Meese said later that was not the case.

"We do not anticipate any changes in the structure or the organizing of the assistant to the president for national security or the National Security Council staff," Meese said.

Meese said the review the president was referring to was a study of the National Security Council's "communications problems" and "coordination problems." Meese said he believes the national security adviser and its domestic policy equivalent have continued to have a "direct relationship" to the president even though both are subordinate to Meese.

Senior White House officials said that while there has been no final decision on what to do about the national security adviser's job, Clark appears to be the frontrunner to replace Allen.

Clark has close and longstanding ties to the president, having served as Reagan's first gubernatorial chief of staff in California -- where, years ago, he first hired Meese into the Reagan official family. Clark, although he had no foreign policy experience before coming to Washington with the Reagan administration, also has the confidence of Secretary of State Alexander M. Haig Jr., whose rancorous disputes with Allen and others became part of the early legend of the Reagan presidency.

Others in the White House and outside it have been urging the appointment of retired Lt. Gen. Brent Scowcroft, who held the national security adviser's job under President Ford.

Allen's fate seemed all the more precarious yesterday, as the president chose to respond in very different fashion to press conference questions about two current investigations of allegations: one concerning Allen and the other concerning Labor Secretary Raymond J. Donovan.

Asked about Donovan, Reagan said he sees no need for his secretary of labor to take administrative leave from his job even if a special prosecutor is appointed to investigate allegations that Donovan's former construction firm made payoffs to union officials in New Jersey.

The president strongly defended Donovan, saying he believed in the "fairness of the American people" and that individuals are innocent until proven guilty. Reagan also said Donovan had personally assurred him he was innocent.

But the president took a different tack when asked about Allen, who has also assurred the president that he is innocent of all wrongdoing -- but who has already placed himself on administrative leave even though no special prosecutor has as yet been appointed in his case. Allen has already been cleared of illegality in the most publicized aspect of his case: the $1,000 he received from Japanese journalists who had intended the money as an honorarium for an interview with Nancy Reagan.

Reagan specifically declined to say that Allen would be allowed to resume his duties if the Justice Department clears him of illegality in the remaining questions about his acceptance of two wristwatches from the Japanese at the time of the interview, and the listing of an incorrect date on his financial disclosure form.

"I cannot and will not answer while an investigation is in process," said Reagan. "I am not going to comment on that in any way."

Reagan said that a review was under way "of not only just one agency or department but all of them -- where you can facilitate things, where you can perhaps loosen something that may have been a bottleneck."

But White House officials later said that there is no large scale review under way and that the prsident was referring to the review of the NSC, which is being done under Meese's supervision.