Dr. Frank E. Young has been head of the Food and Drug Administration for only three months, but he's already trying to move bureaucratic mountains. In addition to coping with current controversies facing the government's oldest health regulatory agency, the commissioner, at 53, is pressing to complete an ambitious "action plan" to "prepare the agency for the 21st century."

Young is taking quite seriously a goal set by Health and Human Services Secretary Margaret M. Heckler at his swearing-in ceremony. He is seeking advice from inside and outside the agency and has sent a videotaped message to FDA's field staff seeking suggestions for the future. Nearly 200 have already come in.

"This activity is the highest priority in the agency," Young said in a recent memo to top FDA officials.

In a recent interview, Young said he has the "most important post in American medicine today . . . . It impacts on 60 percent of the American health care dollar," ranging from the regulation of drugs, medical devices, cosmetics and veterinary products to the safety of the food supply.

Items on his agenda include:

*Prescription drugs. He is pushing to complete the rewrite of regulations governing new-drug approval "very soon . . . . It was a high priority and it wasn't done." Although a Reagan administration proposal was announced with fanfare in 1982, the final rules have yet to be announced.

He pledged to "move heaven and earth" to implement a bill recently passed by Congress to speed the approval of generic versions of existing drugs.

He also said that the agency will review some 5,000 drugs that are being marketed without agency approval, and will step up its review of adverse effects reported after drugs are on the market. The agency is under congressional pressure not to allow a repeat of a tragedy last spring, when an unapproved intravenous drug was linked to the deaths of premature babies.

*Food safety. Young said he believed that the Delaney Amendment, a law requiring that food and color additives be banned if they are shown to cause cancer in animals or humans, should probably be changed to include assessment of how much risk is involved.

But he said he plans to recommend soon that five dyes commonly used in cosmetics be taken off the market because of cancer concerns. He is still studying the evidence on red No. 3, one of the last red dyes on the market.

*Low-calorie sweeteners. He is awaiting a Centers for Disease Control review of complaints about the new sweetener aspartame, but said the evidence thus far doesn't seem to "flag any major problems." He is concerned, however, about relying too much on a single sweetener. "We can't guarantee something is 100 percent safe, so I like a diversity," he said.

*Enforcement. Young pulled out his gold-and-blue FDA inspector's badge to stress the agency's role as safety inspector for the nation's food and drug supply. But he said a recent consumer study charging that the number of enforcement actions at FDA is down dramatically under the Reagan administration is "meaningless" without looking at the whole record.

*Agency morale. Young said that he found agency morale "terrible," in part because of frequent changes at the top, and that he intends to "shake the hands of 4,000 of the 7,000 employes" by the end of the year. Young, a Republican who sold his house and brought his family here last month, said he considers his post professional, rather than political, and hopes to stay three to five years regardless of the November election results.

"The highest calling is really serving the public . . . . That sounds hokey. The problem is, I believe it," he said. "I sense that FDA is moving and really trying to renew itself."

Because of his background, Young puts a premium on improving the FDA's scientific base. Before coming to Washington, he was dean and vice president for health affairs at the University of Rochester, but he is also a microbiologist with a national reputation in genetic engineering studies.

People inside and out of the agency find Young's personal qualifications and enthusiasm impressive. But some headquarters staff have initially found Young demanding and a bit evangelical in his desire to revamp the agency. Another observer worried about his "naivete . . . . He underestimates the political pressures."