THE NOBLE concept of the separation of powers yields plenty of ignoble fights, but few seem quite so base as the one underway at the Department of Energy. Following reports of espionage at the department's nuclear labs, Congress imposed a reorganization of its institutions that will supposedly improve accountability. President Clinton disliked this reform, but this month he signed it into law because it came to him bundled together with popular military pay increases. Having accepted the reorganization, however, the president announced that he would obey its letter but not its spirit. In response, Congress fumes that it may cut salaries or travel expenses for DOE officials.

Neither party comes off well in this fight. By signing a law and simultaneously threatening to ignore its intent, Mr. Clinton has in effect awarded himself a line-item veto more far-reaching even than the one that the Supreme Court recently deemed unconstitutional. This only adds to the strains between executive and legislature. At the same time, however, Congress does not look great. Its effort to promote accountability at the DOE is more likely to dilute it.

In recent years Congress repeatedly has expressed its frustration with the executive branch by tinkering with its institutions. It has pushed the State Department to swallow up the Agency for International Development. It has pushed the Internal Revenue Service and the Census Bureau to accept oversight boards. Now it wants the Department of Energy to set up a semi-autonomous National Nuclear Security Administration to run its nuclear weapons programs.

None of these reforms gets to the main problem at many federal agencies, which is that the multiplication of politically appointed slots has created cumbersome hierarchies. Moreover, the imposition of oversight boards can actually make things worse: They create a new layer of paper shufflers to share responsibility for an agency's performance, thereby diluting the responsibility of the manager who was originally supposed to be running it. Real accountability lies in giving responsibility to one person, who then answers to president and Congress.

Congress's DOE reform repeats this oversight mistake. It gives responsibility for nuclear programs partly to the energy secretary and partly to a new agency chief: In the event of another espionage scandal, each could blame the other. It also creates new bureaucratic complication: Instead of one counterespionage effort, for the Energy Department and for the labs, there will henceforth be two separate ones, and the same goes for all sorts of other functions. Mr. Clinton is right to dislike administrative fission at the DOE. But he is wrong to think that he can sign a law and then get away with flouting it.