National blood-banking organizations are opposed to the Pentagon's decision to require civilian doctors to turn over to the military the names of any active-duty military donors whose blood indicates the presence of the AIDS virus, spokesmen for the organizations said yesterday.

But they said they would accept the new military order reluctantly, in part because a substantial percentage of the local blood supply in some areas comes from military personnel. The military has insisted that the civilian agencies must conform to their policy.

National blood-banking groups, such as the Red Cross, decided to let regional blood centers act autonomously on this issue. They also agreed to give donors prior notice of this new directive.

The order to turn over names to the military came earlier this week when Dr. William Mayer, assistant secretary of defense for health affairs, sent a memorandum to the heads of the armed services and the chairman of the Joint Chiefs of Staff. It said that effective September 1, "all agencies conducting blood collection operations on military installations" must inform military doctors of positive results for screening tests for not only the AIDS antibody, but hepatitis B and syphilis as well.

"The major national civilian agencies collecting blood on military installations have indicated their intent to ask prospective active duty donors to sign a statement giving informed consent for notification to military doctors of positive results and to inform those who do not wish to give consent that they may leave the donation site without providing an explanation," Mayer said in the memo.

Gilbert Clark of the American Association of Blood Banks said, "We've done everything we think can be done to dissuade them from the policy . . . . It will be up to the individual blood centers to deal with this policy." Clark said he was concerned about setting a precedent.

In the past, civilian blood agencies never routinely provided information to military medical agencies about infectious agents found in military blood donors, and tried to protect the donors' privacy.

Some agencies are concerned that medical information released to the military might be used to identify and discriminate against homosexuals and drug users in the military, according to Jeffrey Levi of the National Gay Task Force.

He said that the new policy "represents a backing away from the blood bankers' traditional commitment to protecting their donors."

AIDS antibody information gained from testing in the military's own blood bank programs is already provided to military doctors. The armed services are also considering a new program of widespread blood screening with the AIDS-antibody test.

Dr. Gerald Sandler of the American Red Cross said yesterday that it has 57 regional centers, with some dependent upon military base volunteers for up to l8 percent of their donated blood. Overall, he estimated that about 3 percent of the national blood supply came from military donations.

Julian Barber, assistant to Mayer, said Mayer expects military physicians to protect "confidentiality to the absolute maximum extent consistent with national security."