The number of scientists at the Environmental Protection Agency and the Food and Drug Administration was about the same at the end of President Reagan's first year as it was at the beginning of President Carter's last year, according to the General Accounting Office.

But the GAO said the numbers "mask a definite reversal . . . in both scientific and overall employment." Employment of scientists at EPA went up 4.5 percent in Carter's last year and down 5.6 percent in Reagan's first year, GAO said. Similarly, FDA's number of scientists rose 3.9 percent in 1980 and down 3.4 percent in 1981.

The GAO also checked into the Consumer Product Safety Commission, where it found a 32 percent net decrease in the number of scientific employes. In the case of the CPSC, it said, the Reagan administration accelerated what was already a downward trend during the Carter administration. CPSC lost 12.6 percent of its scientists in 1980 and 22.3 percent in 1981.

The study was requested by Rep. Albert Gore Jr. (D-Tenn.), chairman of an oversight subcommittee on science and technology, who wanted to know if budget reductions were cutting the ground from under the development and enforcement of science-based regulations.

The GAO told him that federal reductions-in-force played a "negligible role" in the declines. Scientists left the government at about the same rate in both 1980 and 1981, it said, but the difference was the Reagan administration did not replace them.