Uncle Sam would pay federal workers in high-cost areas much more than their small-town counterparts under a geographical wage differential system being worked up by the Carter administration.

If adopted, it would mean that Federal scientists, secretaries and administrators in San Francisco, Washington, New York and Boston would earn more than white collar civil servants in areas where costs, and industry wages, are lower.

Despite the proposed change the government would retain as a guideline its national pay scale. That system, which covers most of the government's million-plus white collar employes, has 18 pay grades and 10 longevity pay steps within most of those grades. The national wage scale would be used as a guide or 'index" to determine federal salaries that could and would vary as much as 10 percent to 30 percent from cityto-city.

The proposal now being finished up at the Office of Personnel Management would work something like this:

National pay rates for Grades 1 through 18 would be maintained. They would be arrived at the way they are now, based on annual comparisons of private industry pay on a national average basis.

Using Bureau of Labor Statistics data the government--after setting the national federal rate for each grade--would use that national pay scale giving it an index value of 100.

After local surveys, perhaps in as many as 130 areas with heavy U.S. employe populations, each area would be indexed at above or below the 100 level of the national federal job scale.

Federal wages would be "pegged" at two or more grade levels, representing clerical and managerial or professional level grades. Local federal pay would be indexed at that point, depending on local private wages.

If local industry pay was higher than the government national index of 100, federal employes in that area would be set at the comparable higher level. If it was lower, they would drop below the 100 mark for the national federal pay scale.

Wage experts say that under such a system clerical federal workers in Detroit, for example, might be paid much higher than clerical civil servants in other areas. Government personnel in San Antonio, one of the lowest-cost good-sized cities would get less than the government salary index of 100. Washington area employes could, according to a guessestimate, expect to be indexed at about 103.

Although the national wage level for government pay would change every year,indexing would be done less frequently, probably every three years.

Officials expect heavy opposition from federal unions. But--if they can sell it properly--they might get the support of the bureaucracy, which is heavily urbanized. Although most government employes live and work in high-cost, big city area, much of the union strength comes from southern and western states and military bases.

Insiders say this plan, which still must be cleared by the president, is in lieu of an earlier proposal to split clerical, administrative and technical workers (about 600,000of them) from the regular GS (general schedule) pay system. The current schedule) pay system. The current area wage plan would be set by grades, rather than jobs or occupations.