THE controversy in Washington over the mining of Nicaraguan waters and blame for the American policy failure in Lebanon could obscure a more basic federal institutional concern - how to make government work.
The administration has been talking about the need for ''bipartisanship'' in foreign policy. One could argue it has enjoyed at least quasi-bipartisanship with Congress, in the deals it has made on issues like aid to Central America and deployment of the Marines. And one could note a temptation, in an election year, to portray congressional second-guessing of such agreements as a factor in a policy's failure.
The acrimony already building over such charges in Washington, months before the official campaign gets under way, cannot make it any easier for the White House and Congress to make joint decisions this year, or in a new administration.
But the rhetoric aside, there are some serious questions about how effectively a White House can work with today's Congress, on the domestic as well as foreign affairs agenda.
As David Gergen, former Reagan communications director, puts it in a recent Public Opinion magazine interview: ''If Reagan is reelected, he is going to have to build on the idea of bipartisanship in order to make progress on two central and related areas: deficits and entitlement programs. We are simply not going to get hold of those issues without Democratic and Republican support.''
This is even truer if the apparent likelihood of modest Democratic gains in the House and Senate is realized this fall.
The problem is that Congress is less leadable. The parties as institutions, and party leaders in Congress, have less clout.
Congressional reforms that curbed seniority and committee-chairman bossism in recent decades have made Congress more ''representative'' than ever; that is, individual congressmen are freer to vote their constituents' desires. But at the same time, Congress has become harder to govern.
Election finance changes have made congressmen independent of the party fund-raising purse. Larger staffs permit lawmakers to build their own information and public-relations bases. Television and other electronic communications developments enable congressmen to reach their publics directly, uninhibited by the party hierarchy.
As a consequence, greater skills in coalition-building are demanded today by both the White House and by Congress.
The Reagan administration has tried to deal with this demand on several occasions via special commissions drawn from bipartisan ranks - on social security reform, the MX missile, the Kissinger report on Central America. But there is a limit to the usefulness of this device. It is difficult, as in the case of the MX, to make recommendations stick, even if adopted, through all the steps of congressional review.
For his part, House Speaker Thomas P. (Tip) O'Neill admits he has less direct authority over his Democratic majority than did any of his predecessors, even while observing that Democrats have held together quite closely on party-line balloting the past three years.
From the White House come admissions that the Reagan team, noted for its astute and resourceful dealing with Congress its first year or two, has lost a lot of its finesse and steam on the Hill this session. Too many front-liners have left. The administration should have restaffed at the end of its second year, or at least after its third, insiders say. Some of President Reagan's miscues with Congress in recent weeks stem from faulty liaison work by a team that may be just plain tired, they add.
Recognizing the increasing importance and difficulty of bipartisan action - meaning between the White House and Congress as well as between the two major parties and their regional and ideological subdivisions - political scientist Everett C. Ladd suggests creating a special Cabinet post for congressional and party affairs. This would permit the leaders of both houses in the president's party, who meet now on occasion, to meet on a more regular and structured basis with the president.
Whatever the steps to be taken, and whatever the contretemps over bipartisanship now in Washington, it is not an issue to be dismissed out of hand.