The clear loser so far in the backstage power struggle over national security policy waged over the past month is not Secretary of State Alexander Haig or presidential assistant Richard V. Allen. It is Ronald Reagan himself.

In seeking to avoid conflict, President Reagan unwittingly has reaped confusion. How much confusion was reflected at a National Security Council staff meeting when the new Soviet expert Dr. Richard Pipes (formerly of Harvard) asked NSC staff director Allen: "What I want to know is, what am I supposed to be doing here?"

Amid the confusion of more than 30 interagency committees dealing with national security that are chaired by the State Department, the president still has no plan for crisis management. The conscious downgrading of Allen to avoid the NSC-State Department hostility of the past and make Haig the self-styled "vicar" of foreign policy has left the president's interests unprotected and vulnerable.

The extent to which this has happened became clear in an NSC staff meeting when Allen was urged by his assistants to obtain "rough draft" cables, written in the State and Defense departments, before they are dispatched to diplomatic posts abroad. Allen's repay stunned his staffers. Reading cable traffic was often boring and time-consuming, he replied.

In fact, Allen knows all too well that cable traffic is the lifeblood of policy. Under any of his predecessors, no cable of significance was allowed to leave the United States without first being cleared by NSC staffers.

Allen's problem is not ignorance but weakness. Haig, backed by the Reagan dictum of State Department precedence in policymaking, decided on his own not to clear his cables with Allen. Reagan and presidential counselor Edwin Meese, Allen's boss, almost certainly would support Haig in any showdown over cables. To challenge Haig on cables. Allen fears, would invite defeat.

Allen's separation from cable traffic is a symptom of the threat to President Reagan in a national security staff system forced to cede its true function: protecting the interests of the president. Far worse, despite weeks of back-biting over Haig's control of day-to-day NSC staff work, the question of "crisis" management has still not been decided. That is shown by the fact that Vice President George Bush has now become a possible candidate for that important role.

"Crisis" management is quick handling of unexpected trouble such as the Mayaguez affair during the Ford administration. Under every previous NSC arrangement, Allen would supervise the U.S. response, pulling together conflicting strategies of the departments, as Henry Kissinger and Zbigniew Brzezinski did in their day.

But Allen has been downgraded so far by Reagan's dictum that, as one national security specialist told us, it would be "unnatural" for him suddenly to seize the helm in a crisis. Since Haig is perceived as having a parochial interest to protest -- his own department -- Meese is known to be considering Bush as a compromise.

But Bush would be most improbable as a crisis manager, despite sometime experience in intelligence (CIA director) and diplomacy (ambassador to the United Nations and China.) He lacks authority over the departments, is not a full partner in the NSC committee system and is charged with numberous political chores for the president incompatible with national security. The continuing inability of the White House staff to resolve this question is a time bomb for Ronald Reagan compounded by his own inexperience with national security.

At one Reagan meeting with a visiting foreign leader, Allen barely gained a seat at the table. By such downgrading of his national security assistant, Reagan has insensibly downgraded a system of selfprotection 30 years in the making. This is the real source of trouble, not Allen's well-publicized opposition to Haig's selection of ex-Kissinger deputy Lawrence Eagleburger as an assistant secretary of state.

For the time being, Reagan must hope that no sudden crisis arises. But insiders predict that when the president realizes the consequences of what he has done, he will rehabilitate the NSC system. That means granting Allen the authority he needs to coordinate national security for Reagan while leaving Haig as the nation's chief diplomat.