More than half of Washington's independent pharmacies have withdrawn from the city's Medicaid program charging that they can no longer supply medications to the poor at the reimbursement rates set by the city in 1972.

The 35 pharmacies filled about one-third of the 1 million prescriptions filled last year under Medicaid, the joint locally-federally funded program that pays for health care for the indigent.

As of yesterday, 32 of the independents as well as the 60 chain drug stores in the District of Columbia were continuing to supply Medicaid card holders at a reimbursement rate of cost plus $1.80 per prescription.

The pharmacists received a 20-cent payment increase in 1972, but Dale Morton, of Morton's Pharmacy Inc., 301 Pennsylvania Ave. SE, called that increase "a bone the city threw to the pharmacists."

Morton, who has been speaking for the independent pharmacies, called their refusal to participate in the program a "job action," and accused the city of a "total lack of compassion" for the problems of the pharmacists.

Albert Russo, director of the city's Department of Human Resources, the agency responsible for the administration of the Medicaid program, said his department is preparing recommendations for Mayor Walter Washington regarding increases in Medicaid payments for all health care professionals, including pharmacists.

According to Peter Coppola, director of the Medicaid program in Washington, the pharmacists are the only group to receive any increase in Medicaid reimbursement since the program began here in 1968.

According to Morton, it costs pharmacists in the city an average of $2.59 to fill a prescription. That figure includes overhead, paying personnel, labeling, providing the container and the preparation of the drug. It does not, said Morton, include the cost of the drug itself.

"I had a choice between going out of business in the long run, raising prices to my cash customers or getting out of the Medicaid business," said Morton, who chose the later course of action.

Morton said that the reimbursement level is only one of many complaints the pharmacists have against DHR. Another major problem, he said, is the fact that drug wholesalers are demanding payment twice a month, while the city takes an average of 60 to 90 days to reimburse the druggists. That delay, said Morton, creates much more serious problems for the independents, with their smaller stocks, than it does for the major chains.

According to Coppola, the city reimburses "clean bills" - bills with no complications - within 30 days.