The folks at the Council for Excellence in Government are at it again. Two years ago, just in time for the Reagan-Bush transition, they put together "The Prune Book: The 100 Toughest Management and Policy-Making Jobs in Washington." Now they're gearing up for their second "Prune": "The 60 Toughest Scientific and Technical Jobs in Washington."

Not surprisingly, the director of the National Institutes of Health and commissioner of the Food and Drug Administration made the council's "Science Sixty" list. The NIH has been without a director since James B. Wyngaarden left a year ago and FDA has been without a chief since Frank E. Young departed nine months ago.

The fact that the two jobs are taking so long to fill has set off alarms in science and business circles, where many specialists argue that without strong leadership the agencies will become candidates for neglect on Capitol Hill and at the White House.

The council's list includes jobs not only from the Cabinet departments and big agencies but staff jobs on Hill committees and at the General Accounting Office and Congressional Research Service.

Council vice president John H. Trattner, who wrote the 1988 "Prune," will write the science and technology sequel.

The council is working with the Carnegie Commission on Science, Technology and Government on the project.