Manuel D. Plotkin, who headed the Census Bureau for nearly two years, submitted his resignation yesterday amid reports of White House concern over the handling of the coming 1980 census.

Sources said President Carter called Secretary of Commerce Juanita M. Kreps to convey his questions about the bureau's leadership and its ability to manage the massive decenial count.

Kreps then began her own investigation and was told that while Plotkin, a former official of Sears Roebuck and Co., was excellent as a researcher, he was not providing decisive leadership and that morale in the bureau was low, the sources said.

The decennial census is the single most important function of the bureau, which is a part of the Commerce Department. The population count literally determines much of the allocation of some $50 billion in federal funds under more than 100 programs.

Blacks and Hispanics have repeatedly expressed fears that the 1980 census will fail to count minorities adequately. In the 1970 census, the bureau has said, it failed to count 7.7 percent of the black population.

Last month, the U.S. Conference of Mayors was so concerned about the issue that it appointed a special committee to evaluate the bureau's new efforts to avoid an undercount. Atlanta Mayor Maynard Jackson, a black, was named head of the committee.

Yesterday Plotkin, 55, issued a statement saying he was resigning "in order to avoid a conflict of interest which might result from a lawsuit recently filed by Sears Roebuck and Co. against a number of federal agencies, including the Bureau of the Census."

Sears, facing a federal complaint that it has discriminated against women and minorities, filed suit Jan. 24 charging, among other things, that the Census Bureau's labor statistics are inadequate for measuring compliance with equal employment requirements.

Plotkin said he came to the bureau on a leave of absence from Sears and had agreed to abstain from taking part in any matter involving the firm.

He added that his resignation would be effective at a date "to be determined in consultation with the secretary of commerce." A source said that would be "April 1 or sooner."

Kreps said in a statement that Plotkin had provided "excellent leadership to the bureau" and that his will-ingness "to avoid even the appearance of a conflict of interest is typical of his high standard of integrity and his dedication to the public trust."

Sources said the administration is conducting an intensive search for a successor to Plotkin. One candidate, they said, is the 55-year-old deputy director, Robert L. Hegan, who has talked of retiring. Several other top Census officials have recently retired or are planning to do so.