IT WILL be very tempting for the coming administration to endorse President Carter's recommendation of an immediate 16.8 percent pay increase for top federal officials and removal of limits on their future raises. The direct benefits to the Reagan team and the boost for bureaucratic morale could outweigh concern about undercutting campaign promises to cut federal spending and control inflation. Moreover, recent pay caps have left senior officials earning no more than many of their subordinates. And some federal retirees now receive pensions that exceed what they would take home if they were still working.

But arguments of this sort deserve closer inspection. All executive salaries are not too low; rather, some other elements of the federal compensation system are too generous, and it is this fact that accounts for some of the troubles regularly attributed to low salaries at the top in government.

The recent Advisory Commission on Executive, Legislative and Judicial Salaries claimed, for example, that more senior administrators are leaving government because of the pay cap. But a large part of this exodus has been caused by the fact that retirees are able to combine generous pension benefits with modest earnings from private consulting and lots of leisure -- not because they can command higher fulltime salaries in the private sector. And to some extent the small distance between executives' pay and that of their subordinates arises because many lower-level federal workers are overpaid.

Both circumstances grew out of past procedures for determining federal compensation. Pay increases have been justified on the basis of comparisons with private salaries that exclude many relevant occupation groups and ignore the generous fringe benefits, automatic "step increases" and, most important, the security that government work provides. And pensions and other benefits continue to be suited to a time when they were the major attractions for an otherwise underpaid bureaucracy.

To be sure, there are real impediments to the recruitment and retention of some professionals such as doctors, actuaries and engineers. And there are a few direct management jobs -- running Social Security and the Internal Revenue Service -- that are as tough as any management job in the private sector. There are, as well, hard-working people who deserve individual raises throughout the ranks. But more selectivity in setting pay scales and wider use of the recently established senior executive bonuses and merit-pay provisions would be a better and cheaper solution than general pay boosts.

As for the top political jobs, overly tight conflict-of-interest rules are a much more severe inhibition than pay. Adjustment in federal executive pay -- and, as a separate matter, congressional and judicial pay -- is necessary. But the amounts the president is talking about are all too high. The entire federal compensation system needs to be reviewed.