Washington — While questions pile up at the White House door about the Richard Allen affair, the top White House staff prefers publicly to say it does not see them. The White House is keeping, as best it can, its public distance from an FBI inquiry into Mr. Allen's possibly improper receipt of gifts and exchange of favors with Japanese friends and clients.
At some point, President Reagan himself may have to step in.
More positively, some Reaganites see in the Allen affair opportunities to resolve the bickering that has gone on between the White House and State Department, to strengthen the White House national security staff, and to free a bottleneck at the top staff and Cabinet level where the President gets his final input before making crucial war-and-peace decisions.
The questions piling up begin with whether Allen, the national security adviser, accepted $1,000 - or $10,000 - and two watches for setting up an interview for Japanese journalists with the President's wife, Nancy. They include whether Allen improperly continued to aid former Japanese clients during US-Japan auto import negotiations last spring, and whether his former consulting firm (now run by Peter Hannaford, a former business associate of Michael Deaver, who is now one of Mr. Reagan's closest advisers) has been able to benefit from his influence. Messrs. Deaver and Hannaford had run President Reagan's financial affairs for several years.
Another question: Did White House Counselor Edwin Meese III act properly in contacting the Justice Department about the case. Mr. Meese supposedly cleared Allen - a member of his White House policy staff - of questions raised about Allen's Japan links during the election campaign.
Thus the Allen affair brings into question the judgment and associations of two of the President's three top aides and his national security adviser, as well as opening the President's wife to possible FBI questioning.
Yet the White House press have received mostly ''no comment'' from officials, who have left it up to Allen himself to answer reporters' inquiries.
The pressures are mounting to review not only Allen's position, but to rethink the national security and foreign policy tie-in at the White House, and the quality of the White House national security staff.
''It doesn't look good at all,'' says one administration source. ''They should never have brought Allen back from the campaign. If the story is going to continue to dribble out like this, it's going to make everyone look bad.
''If Meese were smart, he'd do a reorganization on his own and find a candidate to replace Allen on his own.''
The administration's ''bottleneck'' problem, quite apart from the Allen affair, is readily observed by foreign policy experts. The bottleneck is described as the Meese counselor position, through which both the national security adviser and State Department must work.
Says Theodore Eliot, dean of the Fletcher School of Law and Diplomacy at Tufts University in Medford, Mass.: ''It's unusual to have the principle foreign policy guy go through somebody else to the president. This is certainly another complication in the organizational framework.''
And to have the Meese position ''between the secretary of state and the President makes it more difficult, because there are more senior players than before,'' Dr. Eliot says.
Meese, with his national security and domestic policy staffs, is not regarded by Reaganites as having put together as strong an administrative team as has White House chief of staff James Baker III.
However, ''Ed Meese is not going to be a goner,'' says one administration official. ''He's in trouble as an administrator. Baker has a lot more good people in place in the government. Meese doesn't have a lot of strong people around him.
''But Meese is still very close to the President. He's still a very good synthesizer of the issues for the President.''
Questions involving personnel are difficult for President Reagan to confront, say those who know him well.
''There may have to be tough decisions and basic reorganizing,'' says one administration source. ''People are looking at that right now. For it to happen would require a different philosophy among the people closest to the President.
''There's no question that it is being discussed. You're not going to see a reorganization soon. You wouldn't see one until after the first of the year, or maybe by spring.
''Whether it gets accomplished is another thing. These are very tough decisions. The President does not like that kind of personnel decision. You have a president who's never going to call in his people and say, 'Look, I want A,B,C ,D, and E,' '' the longtime Reaganite says. ''What you need around him is someone who says, 'Get him A, B, C, D, and E.'
''Meese is very good at saying 'These are the things facing you today, Mr. President.' He puts them in Ronald Reagan's language and the choices for him in Ronald Reagan's language. But you don't have anyone coming to him and saying, 'This is what you ought to hear.' ''
Reagan's role at the moment includes the Allen affair but goes beyond it, expert observers say.
''What to do when a National Security Council director is under a cloud?,'' asks Eliot. ''The president has to make that decision. And in the final analysis , only the president can make decisions on what kind of apparatus he wants.''