The American Medical Association, long lukewarm or hostile to prepaid medical care, yesterday endorsed a report organizing prepaid health plans as legitimate competitors of the usual fee-for-service doctors.

But the AMA House of Delegates, meeting in Chicago, deleted a key recommendation of the AMA's own Council on Medical Service -- one saying the AMA should "recognize" that prepaid plans may cut costs.

Cost-cutting is a main argument for the plans, which have been called health maintenance organizations (HMOs), ever since the Nixon administration started pushing them to try to cut health costs.

At the same time, however -- and rather confusedly -- the AMA delegates approved a Council of Medical Services report, an HMO study two years in the making, as "an objective assessment."

That report concludes that "many" HMOs have provided care at a savings. It says "several studies" have shown the HMOs have "a generally lower rate of health care expenditures," mainly by sending their members to the hospital less.

The AMA action was thus seen by HMO supporters as a boost.

Since the Nixon administration started backing them, these plans have grown phenomentally. There were only 37 in 1970. There are 240 today, including 13 new ones this year, and many major employers are advocating them.

Dr. Robert B. Hunter, the AMA's new president, said in an interview he was "sorry" the delegates deleted the cost-saving clause and referrred it to the AMA's trustees for more study.

He nonetheless saw the council report and delegates' approval as recognition that HMOs are part of medicine's future. A family practitioner in a town 75 miles north of Seattle, he is a member of an "IPA" or "independent practice asociation," an "HMO without walls" in which independently practicing doctors associate to give prepaid care.

"All our county's doctors belong," he said. "We've had IPAs in our state since 1934. We insure about half the state's population and feel it's cost-effective."

Still, Hunter, like the delegates, said HMOs should be "only one part of a pluralistic system." The delegates urged "fair market competition" among health systems, as well as "neutral public policy" without "federal advertising promotion" or federal subsidies to help HMOs grow.

Between 1975 and 1979, a federal HMO office gave $235 million in grants and loans to help start HMOs. This fiscal year the the sum will be another $156.8 million, and $205.9 million more is budgeted for fiscal 1981.

But federal rules, many of them ordered by Congress, have also hindered some HMO growth, said Dr. Walter McClure of InterStudy, a Minneapolis study group that has played a major role in spurring HMOs.

"I think public awareness of the HMO idea has had more effect than federal action," he said. "We're urging that federal funds be concentrated to help start HMOs in areas where just starting one will trigger private development of others."

In other actions, the AMA delegates:

Said doctors and the public should try to discourage tobacco ads in newspapers and magazines.

Urged states to establish waste sites for disposal of low-level radioactive wastes, since the high cost of disposal, at only three sites in the nation, threatens valuable nuclear diagnosis and research.