Mr. Allen's job

Richard Allen has acted judiciously in taking an ''administrative leave of absence'' while the FBI completes its investigation into his receipt of some cash from a Japanese magazine.

The national security adviser ostensibly requested such a leave in order to be free to speak out and answer questions in public. But pressures clearly were building up on him within the White House to take some step at this point.The Allen affair is potentially the most damaging and embarrassing of President Reagan's personnel problems, and there is little doubt that Mr. Allen's departure is greeted with some relief.

This should not in any way imply guilt of wrongdoing. Mr. Allen has forthrighly admitted to ''bad judgment'' in his handling of the $1,000 ''payment'' or ''gift'' or whatever it was. Indeed it was at the least bad judgment to have accepted the money in the first place and then not to have turned it over at once.

But fairness and justice demand that Mr. Allen, like any other individual, be given the benefit of the doubt and be presumed innocent unless the federal inquiry determines otherwise. The press, even while probing the story, should be careful not to contribute to unsubstantiated reports or to circulate ''innuendoes,'' as Mr. Allen has described them.

In this connection it rests on the FBI to handle the case expeditiously. Inasmuch as the investigation was begun back in September it seems somewhat odd that a determination has not yet been made whether to call for a special prosecutor. Besides the cash payment (and the exact amount of money involved), questions have also been raised about Mr. Allen's continuing contacts with former Japanese business associates and the sale of a consulting business to a former Reagan aide.

These may all prove to be, at worst, improper behavior for a high public official. But in any case it would be regrettable if the administration were perceived to be dragging its feet - or opened itself to criticism for perhaps resolving the matter during a holiday season when public attention was fastened on other things. The sooner the FBI acts, the better.

Mr. Reagan doubtless hopes Mr. Allen will clear himself. But, beyond the propriety or legality of his conduct, lies the question of Mr. Allen's suitability for his present job. That, too, will have to be weighed by the President.

By all accounts, the National Security Council has not been run with a firm hand and has not performed effectively. That is a serious concern, for Mr. Reagan very much needs an experienced professional who can help sift, coordinate , and present positions within the administration.

Every president works out precisely how he wants this advisory task performed , and no two presidents have operated alike. But the job has to be done well.

The present weakness of the NSC has led to certain inconsistencies and confusion in the conduct of foreign policy which Mr. Reagan will want to correct. Perhaps the need is not for someone with political influence to rival the secretaries of state and defense or other Cabinet officials but for an efficient, knowledgeable administrator of the caliber of a Brent Scowcroft, say, who would provide good staffing for NSC meetings. The NSC would then be primarily an administrative not a policymaking body.

In any event, the time has come to bring better order to the foreign policymaking structure. The Allen affair makes this abundantly clear.