Although the Reagan administration has scaled down the public and private stature of the White House national security affairs adviser -- as compared to the heyday of Henry A. Kissinger and Zbigniew Brzezinski -- it is now clear that even this new low-profile version remains close to the powerful center of government decision-making.

For example, when recommendations go to President Reagan from Cabinet officers on national security matters, they usually go in with a covering memo from Reagan's national security affairs adviser, Richard V. Allen, pulling the various elements together and explaining to the president, in brief, what he is about to look at.

Allen's job for the president, as he explained it during an interview in his office in the White House's West Wing, is to make sure that the Cabinet views show all the options available to the president, and, later, to make sure the decision is implemented. "In the event an option is not fully explicated, or points are missing," Allen adds, "it is our job to fill them in."

In an administration designed around Cabinet government, that ability to fill in what may be missing from Cabinet recommendations is a key indicator that power still resides in the national security adviser's office.

To help Reagan further with the kinds of long-range studies that the rest of the government involved in daily operations seldom has time for, Allen has assembled a 64-member staff that is a mixture of like-minded conservative colleagues, academics, military officers, former CIA officials and foreign service officers.

Allen, a soft-spoken, gray-haired 45-year-old with hardline views about the Soviet Union and U.S. foreign and defense policy, meets with Reagan at least once a day and briefs him about national security matters. the staff that Allen presides over is that of the National Security Council (NSC), the nation's highest decision-making body and chaired by the president.

Last December, when then president-elect Reagan named Allen as his assistant on national security, Allen told reporters: "You are seeing a disappearing act right now."

Reagan's idea, which Allen shares, was to end the confusion in this government and others that sometimes occurred when Kissinger or Brzezinski, rather than the secretary of state, spoke out forcefully and publicly on controversial policy issues.

"The secretary of state will be the president's principal spokesman and adviser" on foreign policy matters, Reagan said. The national security affairs adviser, it was said, will revert to the more invisible, behind-the-scenes role of the Eisenhower years, limited mostly to coordinating the views of the bureaucracy.

"After nine or ten weeks," Allen says, "I think we are in pretty good shape. we are up and working and on the right track."

But despite his own and the White House's efforts, Allen and his staff have not quite disappeared. In fact, they have become increasingly visible lately. Furthermore, some critics are not sure the system is working well and so the role of the adviser and staff is once again becoming a subject of debate within government.

On March 21, Allen delivered his first public speech since taking office. It was a controversial one, pointing to concerns about pacifist sentiment in some quarters of Europe. Though visiting Europeans acknowledge this is so, the speech is known to have annoyed the State Department, which had not seen the text first, and some U.S. allies.

A few days earlier, Richard E. Pipes, a Soviet expert from Harvard University and a senior member of Allen's staff, also expressed some controversial views in an interview that he apparently thought was off-the-record.

Pipes reportedly suggested that detente was dead, that economic problems eventually would confront Moscow with a grim choice between reforming its system or going to war, and that the West German foreign minister might be susceptible to Soviet pressures. The State Department quickly moved to disavow Pipes' remarks.

It is something of an irony, therefore, that while the new administration has laid heavy emphasis on speaking with one voice and submerging the once powerful office of the national security adviser, the first few times public attention has been focused on that office it has been over controversy.

Allen's operation has also become more visible because the new administration includes a dominant personality, Secretary of State Alexander M. Haig Jr.Some of the squabbles for turf set off by Haig or those trying to contain him have caught the NSC in the middle and spilled into public view.

But a larger question now surfacing within the defense and foreign policy sector of the government is whether it is possible to go all the way back to the days of a down-rated White House national security adviser and staff.

Beyond that lies yet another question. If the security adviser should play a more forceful role, is Allen, who remains more of a mystery man to the bureaucracy than his more outspoken predecessors, able to play it?

A White House official, with many years of experience in government, says there is "good news and bad news" about Allen's operation so far. The good news, he says, is that the president is kept actively engaged in national security matters and well informed by Allen. "When the president comes to an NSC meeting, he is tuned in and knows what's going on. So the president personally is well served," the official said.

But the bad news, he adds in a complaint that is rather widespread among agencies outside the White House, is that the administration itself is less well served. Allen and his staff, he says, seem primarily a collection of individualists rather than organizers and have not yet come to grips with trying to coordinate the actions and integrate the recommendations of the various foreign policy and defense branches of government.

The result, a number of officials claim, is that, rather than orderly and timely decisions, many are either delayed or made too hastily because one department has not had time to absorb the views of another.

Though Allen denies it, several officials believe the decision to postpone, for the first time in eight years, a semi-annual consultative meeting with the Soviets in Geneva on compliance with the strategic arms treaty was one that was made in a less-than-deliberate fashion.

Other officials suggest recent internal NSC deliberations on aid to Pakistan and on a controversial military sales package to Saudi Arabia tended to be driven more by approaching events, such as the return of the U.S. ambassador to Pakistan in March and Haig's trip to the Middle East this month, than by early consideration of other factors.

"The system cries out for a stronger role for the NSC," meaning Allen and his staff, one official says, "but they are not grabbing for the leadership mantle. After the first real foreign policy crisis," the official adds, "when they see they have to coordinate better the activities of several departments, they [meaning the White House] will see it needs strengthening."

As matters stand now, the NSC has been meeting at least weekly. Below this level, a system of senior interdepartmental groups (SIGs) chaired either by the deputy secreatary of state, defense or CIA, has also been set up, with Allen having some authority to steer problems to an appropriate official in areas where it is less than clear who should lead the group. Below this is an interdepartmental working group, or IG, that does the groundwork for the SIGs.

What all this adds up to, many officials complain, is a seemingly endless round of meetings preparing for still higher-level meetings.

Allen, unlike Brzezinski or Kissinger, chairs none of these groups. Critics claim the White House therefore loses some of the control it should have. Because of the many foreign policy issues that have come up in the early months of this administration, State has headed most of the SIGs and IGs. But some officials complain that State's paperwork is sometimes slow getting to others in government, limiting the quality and time of the responses.

Whatever the ultimate status of Allen's operation, one thing is clear. He is a team player in an administration that puts a very high value on teamwork rather than individual performance and credit-grabbing.

While Allen is criticized by some as too passive for a job that needs somebody to push Cabinet officers occasionally, he knows how the president likes things done and therefore can be a formidable ally or opponent.

Allen has tended not to try and tackle Haig on any of the internal controversies that have cropped up. Rather, higher-level White House officials who have Cabinet rank, Edwin Messe III and James A. Baker III, have sought to work things out with the secretary.

Allen acknowledges some normal setting-up problems, but he says internal coordination is smoother than it is pictured in the press and relations with State are good.

In fact, he says, reducing the visibility of the staff and removing it largely from daily problems actually increases its importance because it can focus on detailed studies of where U.S. policy should wind up two of four years from now. Such studies on the Middle East, U.S.-Soviet relations and policy toward Asia are under way, he said.

Allen's No. 2 man is retired Navy rear admiral James W. Nance, among the most well-connected military officers in Washington, having worked for both Haig, when the former general was NATO commander in Europe, and for Sen. Jesse A. Helms, the powerful conservative Republican from North Carolina.

Allen had divided his professional staff into four groups. Military affairs is headed by an active-duty Army major general, Robert L. Schweitzer, who also worked for Haig in Europe.

Political affairs is headed by James R. Lilley, who spent 27 years with the CIA, becoming the top intelligence expert on China. Since leaving the CIA a few years ago, Lilley, who was born in China and whose father was with Standard Oil's operation in China for 26 years, has also done consulting work for Hunt-SEDCO, a U.S. firm involved in off-shore drilling rights near China, and for United Technologies Inc., Haig's former firm.

The intelligence section is headed by Donald Gregg, a former NSC staffer on loan from the CIA. Gregg, who spent 18 years in Asia, will also be handling a portion of East Asian affairs.

No head has been named yet for the fourth group, planning and evaluation.

Among the other key players is Pipes, who Allen calls a "first-rate intellect who belongs in this administration" despite the "unfortunate" flap over the interview. Pipes wil focus on the Soviet Union and Eastern Europe.

Carnes Lord, a former assistant professor from the University of Virginia, will be looking after global strategy and doctrine as well as U.S. government broadcasting operations overseas. Geoffrey Kemp, from Tufts University, will be watching the Persian Gulf and Middle East. Fred Wettering, a State Department foreign service officer with four tours of duty on Africa, will handle sub-Saharan African affairs.

Roger Fontaine, from Georgetown University's Center for Strategic and International Studies, will be the senior specialist in Latin American affairs. James Rentschler, an NSC staff holdover and foreign service officer, will handle Western Europe and some northern African affairs. Another military officer, Army Maj. Robert M. Kimmitt, who is also a lawyer and served previously as a counsel on the NSC staff, will handle arms transfer matters.

The senior staff members in the international economics area are Rutherford M. Poats, who served on NSC during the Carter administration and was also the head of a private overseas investment firm, and Henry R. Nau, an associate professor at George Washington University.