Prince George's County school officials said yesterday that the heavy response that brought in nearly 4,000 applications for the county's magnet school program will enable 25 of 29 magnet schools to meet desegregation goals next year.

As an indication of the success, Superintendent John A. Murphy said the magnet programs had brought in nearly 1,000 applications from students in private schools. School officials said they also were pleased that they could improve upon this year's statistics -- when eight of 12 magnet schools met racial guidelines.

But the unexpected interest that is propelling the program also is creating an unwanted side effect: a long waiting list made up almost entirely of black students unable to enroll in magnet schools because many of the slots are reserved for white students. Of 2,255 students on waiting lists, 2,158 are black.

"That's our dilemma," Murphy said at a news conference yesterday. "The number of options aren't there for black parents as there are for white parents. We have to make those options available."

The superintendent said that when school officials were planning next year's programs they did not anticipate the large number of applicants and therefore had not made plans to accommodate that many students. He added that he would work to open new programs for black students in the 1987-88 school year.

Murphy's "dilemma" stems from the design of the magnet plan, which is being used to draw white students into predominantly black schools by offering special programs, including Montessori, science and math and foreign language schools. In order to integrate those schools, officials say, slots must be reserved for white students.

Achievement of racial goals at these schools will move the county significantly closer to fulfilling desegregation requirements ordered by a federal court 13 years ago.

Of 48 schools that fell outside court-established racial guidelines a year ago, 20 will be within those guidelines next year, according to officials. Five others will be meeting a timetable for desegregation submitted to the court by school officials. Fourteen schools not participating in the magnet programs will receive additional resources. Officials say those schools cannot be desegregated because of their distance from white neighborhoods. Boundary changes and new programs in the 1987-88 school year are expected to bring the remaining schools within guidelines.

"If these projections hold and everyone comes on the first of September, we will be more than two-thirds of the way to fulfilling the court requirements," said school spokesman Brian J. Porter.

Of the county's 103,000 public school students, about 4,900 will be participating in magnet programs next year. Porter said officials did not anticipate the large response based on the experience of other systems, where it took several years before magnet programs accomplished desegregation goals.

The magnet programs, which were introduced last September in 12 schools, were popular from the beginning. This year, after black parents complained that they could not get their children into magnet schools for gifted students, two new programs were opened for those children in predominantly white schools. Murphy said a similar approach will be taken with other magnet programs.

While officials acknowledged the problem of many black students on waiting lists, they also argued that more black than white students are being served by the program. Students already enrolled in schools offering magnet programs -- most of whom are black -- were automatically admitted into the magnet courses at those schools if they applied, so 56 percent of the students enrolled in magnet programs are black, officials said.

Nonetheless, black leaders in the county were dismayed by the waiting list, which consists of black students hoping to transfer to schools where magnet programs exist. "It's very distressing. You're going to have to give a certain priority to white students, but it shouldn't be this bad," said Maryland Del. Albert Wynn (D-Prince George's), who is a member of an organization that was formed in response to the desegregation controversy.

The waiting list may contribute to a perception in the black community that the magnet program is benefiting white students disproportionately, said Alvin Thornton, who sits on a citizens committee established to advise Murphy on the program.

"They're going to perceive that their kids are in distinctly inferior programs," he said of families on waiting lists. "That is the problem."

School officials said the waiting list will serve as proof that there is interest in new programs and will help win additional funding to open those programs.

"We realize it's incumbent upon us to move very quickly," said Porter. But he added that the large number of applicants has "reassured" officials that "the goals of the school system are supported by the community."

Parents showed the most interest in the science and math programs and the so-called traditional academy, where students will wear uniforms, study a basic curriculum and be held to stricter discipline codes, according to officials. There are still openings for nonblack students in science and math programs, foreign language immersion, traditional academy and "extended day" programs, which offer before- and after-school day care.