The country's principal agency for identifying and controlling the spread of infectious diseases is facing severe budget cuts that could cripple many of its important programs, according to federal and state health officials.

These officials fear that 1982 budget cuts sought by the administration, and in some cases further reduced by Congress, could sharply restrict the ability of the Atlanta-based Centers for Disease Control to combat outbreaks of rare and common diseases, from Legionnaire's Disease to the annual waves of flu.

Under pending 1982 budget proposals, in limbo under the continuing budget resolution set to expire Dec. 15, the CDC's Center for Infectious Diseases could undergo funding cuts ranging from 35 to 59 percent, knowledgeable officials say.

CDC Director William H. Foege already has announced that the CDC will have to lay off between 350 and 780 of the agency's 3,700 employes. Under present plans, sources say that half of those layoffs will come from the CDC's infectious diseases center, which has the largest staff of its seven units.

Public health officials expressed concern that if the programs the CDC is considering curtailing or eliminating are actually cut, they will be unable to pick up the slack in their respective states.

"CDC is a national resource for not only the surveillance of these diseases but also for the preparation of diagnostic tools that cannot be replaced by the individual states and cannot be replaced by private industry," said Dr. William J. Hausler Jr., director of Iowa's environmental and public health laboratory.

Dr. George Anderson, president of the Association of State and Territorial Public Health Laboratory Directors, called CDC "the main bulwark we have in this country against major disease problems . . . . We have to have a central focal point in this country that is well-staffed and able to respond quickly to these types of problems."

Dr. Charles D. Cox, a University of Massachusetts microbiologist and an official of the American Society for Microbiology, warned of a "national crisis" if the CDC is unable to provide states with essential diagnostic tools needed to identify unusual organisms.

Cox and another official of the society recently wrote to the Senate Appropriations Committee to complain of "the seriousness of the impact on the public health and safety" resulting from proposed reductions.

A recent budget document prepared by the CDC for the Congress on the impact of proposed cuts, obtained by The Washington Post, indicates that the following changes are under consideration:

The CDC program to provide commercially unavailable chemical reagents required for diagnosis of newly recognized organisms such as that responsible for outbreaks of Legionnaire's Disease would be reduced or eliminated, "thereby slowing down identifying and controlling infectious disease agents." The document indicates that the "only reagents" for the diagnosis of dengue fever, a viral disease transmitted by mosquitoes, would no longer be supplied.

The hospital infections control program could be "completely eliminated." The program is described as the "sole national resource" for helping to combat the 1.5 million annual cases of hospital-acquired infections, which in turn result in an estimated cost of $2 billion annually in extra hospitalization.

CDC would not be able to proceed with projects involving the newly approved hepatitis B vaccine or studies of hepatitis A, delaying the "payoff for the years of research that have been devoted to these extremely serious infectious diseases," which result in medical costs of about $120 million each year.

CDC Director Foege declined to comment on the specifics, but confirmed that his agency had prepared the document and that "those are all possibilities." He emphasized that "no final decisions" had been made, but that they would need to be made next month. Staff reductions are expected to begin as early as February.

The budget problems are complicated by the uncertainties produced by Congress' failure to pass a Department of Health and Human Services appropriations bill. Although House-passed levels are in many cases higher than the administration requests, the Senate made some cuts that would worsen CDC's funding, health officials say.

Excluding grants and separate funding for the National Institute of Occupational Safety and Health, CDC funds would be cut from the 1981 level of $111 million to a level as low as $90 million under the administration's latest 1982 proposals.