The Department of Health, Education and Welfare has taken charge of the administration's study of the health effects of low-level radiation - a project that may turn out to be the biggest medical research program since the smoking studies of the 1960s.

It could also turn out to be a bureaucratic nightmare, since at least three government departments and another three agencies have institutional or regulatory issues at stake.

The investigation will focus on some 300,000 to 400,000 military and civilian personnel who participated in the government's nuclear weapons testing from the late 1940s through 1964 - when atmospheric tests were halted - and several hundred thousand employes of government nuclear facilities.

The scientific community has long disagreed about the long-term cancer-causing effects of low levels of radiation.

Until late last month, the Department of Defense and Energy were the prime agencies directing inquiries into the effects of radiation exposure on participants in 1950s nuclear weapons tests and on workers in atomic facilities and laboratories.

These inquiries were a direct out-growth of two reports: One that a statistically significant number of GIs who participated in a 1957 nuclear weapons test in Nevada came down with leukemia, a cancer of the blood, the other than an unusual number of former workers at nuclear submarine repair facilities at the Portsmouth, N.H., Naval Shipyard also developed cancer.

Hearings on those situations before a House subcommittee on health and environment last January forced the defense and energy agencies to develop plans to investigate both.

Last month, however, President Carter gave HEW that task and more.

According to a White House memo dated May 9, HEW is to draw up a coordinated governmentwide program that would also:

Insure "that persons adversely affected by radiation exposure receive the care and benefits to which they may be or should be entitled."

Inform people "who might have been affected" by low-level radiation and the public about "steps being taken and the conduct of the studies."

Recommend "steps which can be taken to reduce the incidence of adverse radiation exposure of this type in the future."

The White House staff, according to informed sources, pushed the task on HEW because they did not feel defense and energy were impartial in their approaches.

"Energy looked on it as an energy problem," a Carter aide said recently, "and defense saw it as a defense problem. We wanted it treated as a health problem."

In turning the matter over to HEW, the White House didn't notify two key participants, the Environmental Protection Agency and the Nuclear Regulatory Commission. Both agencies have responsibility for worker and general public radiation standards.

Ironically, when the government reorganization acts of 1970 and 1974 were approved, setting up those agencies, responsibility for establishing governmentwide radiation safety standards was dropped. Today, neither agency has that specific duty.

Those same acts also did away with the Federal Radiation Council, which until the early 1970s coordinated intergovernmental research on radiation.

F. Peter Libassi, general counsel of HEW, now has the task of putting the president's radiation research program back together.

For the past several weeks, Libassi has been getting to know the interested groups both inside and outside government. Watching over his shoulder are environmental and industry groups who look on the radiation study primarily as a vehicle for either attacking or defending nuclear power facilities.

Tentatively, Libassi hopes to give the White House by Sept. 1 an outline of what needs to be accomplished.

There also is a possibility that a new commission will be proposed, for continuing supervision of the intergovernmental program.