Navy Secretary James H. Webb Jr., responding to concerns about a growing brain drain at the Naval Academy, has approved a package of salary increases and bonuses to help recruit and retain top faculty members, Navy officials said yesterday.

Under the package, Naval Academy officials will be able to raise, as they see fit, salaries for entry-level teaching positions to better compete with other universities for top talent. About $250,000 in merit bonuses will be distributed annually among a quarter of the 334 civilian professors. Additional funds will be provided to employ faculty in research projects during the summer.

"This is a great shot in the arm," said William B. Garrett, associate dean for administration, who warned this year that the academy increasingly had to settle for its second or third choice for teaching posts because top candidates were taking better paying jobs elsewhere.

Officials said the pay initiatives will provide the Naval Academy and two other naval teaching institutions with flexibility in dealing with the most glaring deficiencies in their faculties. The Naval Academy, for example, has had trouble recruiting faculty members to teach electrical engineering, mechanical engineering, math, computer science and economics.

"This change is long overdue," said Rep. Thomas McMillen (D-Md.), whose 4th Congressional District includes Annapolis and who is a member of the Naval Academy's Board of Visitors. "Our 'Top Guns' were not getting the top teachers."

For years, the Naval Academy, which produces the cream of the Navy's officers and technical experts, has managed to attract and keep top-level faculty with the allure of teaching at one of the nation's prestigious institutions.

But a fast-widening gulf between salaries paid by the academy and those of virtually every other major university in the country has seriously hurt the academy's ability to recruit civilian instructors and retain those currently employed.

Full professors at the academy receive an average annual salary of $43,200 -- compared with $52,800 at the University of Maryland, $59,000 at the University of Virginia, $55,900 at the University of Michigan and $69,700 at Harvard, according to 1986-87 academic year figures compiled by the American Association of University Professors.

Faculty salaries at the Naval Academy are comparable to those at colleges and universities that lack large research programs, such as James Madison University in Virginia, Central Michigan University and the University of Minnesota-Duluth.

Moreover, under a federally imposed limit, the Naval Academy can't pay its dozen top-tenured professors more than $72,500 a year, a figure far below the top salaries and other financial benefits offered by Ivy League schools and prominent state-supported colleges and universities.

Under the new plan, those senior professors could qualify for merit bonuses on top of their salaries, according to Garrett. Also, the Naval Academy will have wide latitude in raising entry-level salaries, which currently range from $26,472 to $46,754 a year for assistant professors.

The bonuses awarded each year to the most deserving quarter of the civilian faculty would equal up to 15 percent of the professors' salary.

Officials were unable to say yesterday how the package compares overall with an earlier proposal by the academy's academic deans for a 15 percent across-the-board pay raise over three years.