The Reagan administration has proposed new collection standards for a special loan program for medical students that two-thirds of the nation's medical schools -- including some of the most prestigious -- say they will be unable to meet.

Under the proposal, after March 31 schools with a delinquency rate of more than 5 percent in the Health Professions Student Loan program would be forced to drop out. The $246 million program, the largest federal loan program exclusively for medical students, has helped thousands of students, many of them minorities, since its creation in 1965.

Harvard University Medical School and Howard University's College of Medicine have among the highest delinquency rates, according to a spokesman for the Health and Human Services Department. All three Virginia medical schools also could be forced to drop out of the program.

HHS officials contend that the 5 percent rate is realistic and more liberal than the 3 percent delinquency rate that most commercial lending institutions expect when lending to highly paid professionals.

But the colleges claim that the 5 percent rate is unfair because HPSL was created to make loans to students facing "exceptional financial needs." Loans to such students are much more of a risk than loans to established professionals, they claim.

The Association of American Medical Colleges (AAMC), which represents all accredited medical schools, said the standards will "dismantle the HPSL program . . . and reduce the ability of schools to financially assist students, many of whom come from minority groups underrepresented in medicine."

Most medical schools average a 12 percent HPSL delinquency rate, but several have much higher rates. The medical schools at Harvard and Howard are among the five worst in the nation when it comes to collecting overdue HPSL debts -- based on June 30, 1981, statistics, which HHS said are the most recent.

HHS said 31.2 percent of the 777 former and current Harvard medical students with HPSL loans have not paid them.

At Howard, which has the worst collection record, 56.5 percent of the 836 students who owe HPSL loans have not paid them, HHS said. That amounts to more than $500,000 in unpaid loans. The school's dental college reported a 54.5 percentage delinquency rate, and its pharmacy school 62.7 percent.

Georgetown Medical School reported a 3.6 percent delinquency rate and George Washington University Medical School 7.5 percent.

Virginia Commonwealth University Medical College had a 22.05 percent delinquency rate, HHS said, Eastern Virginia Medical School had 13.89 percent and the University of Virginia Medical School 11.1 percent.

Johns Hopkins University Medical School had a 5.2 percent delinquency rate. Figures were not available for the University of Maryland in Baltimore.

Sterling Lloyd, an assistant dean at Howard University's medical school, said the proposed ceiling will "discourage some low-income applicants from applying to medical schools and will force needy students who are currently enrolled to take out larger, higher-interest loans if they are available."

As a result, students "will graduate with high debt levels and will not be able to go into teaching, research or low-income areas to practice," he said.

During the 1981-82 academic year, 175 of Howard's 496 medical students received HPSL loans.

Alice M. Swift, an administrator in HHS's student loan division, said the schools could meet the 5 percent standard if they implement the debt-management techniques that the agency has proposed. They would require schools to join credit bureaus, hire private collection agents, file legal action against debtors whenever possible and submit quarterly progress reports to HHS.

The government has issued HPSL loans to 83,111 students since the program was created. Currently, 46,686 loans are being repaid, HHS said, and 6,698 loans -- worth $19.4 million -- are in default.

The HPSL program was the primary federal lending unit for medical students during the 1960s and '70s, but it is not the major source for medical students now. During the 1981-82 academic year, 66,298 students were enrolled at 126 medical schools, according to the AAMC. Those students received 44,000 Guaranteed Student Loans worth an average of $4,900 each; 4,700 Health Education Assistance Loans, which averaged $7,050 each, and 10,245 HPSL loans, which averaged $2,375 each, according to the AAMC. Overall, more than 70 percent of medical school students received some type of government loans, AAMC said.

Officials said the government is receiving payment on $13.8 billion in GSL loans, with $1.7 billion of those loans in default. Officials claim, however, that the overall delinquency rate for the program is 5.8 percent because much of the $1.7 billion will be collected. The HEAL program doesn't list delinquency rates.

The HPSL program differs in that it is a direct-grant program. The schools match the government on a ratio of one school dollar for every nine federal dollars. That pool is the school's loan fund. The GSL and HEAL programs simply guarantee loans made through commercial institutions.

The Reagan administration has not been sympathetic to medical loan programs, believing that medical students should find other ways to finance their education.