Dr. W. E. Matory, the Washington physician with the highest fee listed in a new Nader guide to Medicare doctors, said yesterday that he raised his rates in an effort to collect more money from the federal health insurance program for the elderly.

The higher fees do not immediately increase the amount that Matory, a general surgeon and university professor of surgery, receives from Medicare or from his patients. What they do is raise the "fee profile" that Medicare creates to help it determine reimbursement rates.

Matory's customary charge for performing some types of intestinal surgery in 1978 was $2,000 -- nearly twice as much as some other local surgeons charged for that procedure, according to the Nader guide, "Your Money or Your Health: A Senior Citizen's Guide to Avoiding High Charging Medicare Doctors."

Matory did not collect the entire $2,000, because Medicare sets an areawide ceiling payment for that procedure of $1,069.50. Medicare pays the doctor $807.60, or 80 percent of the ceiling. The patient is responsible for $261.90 -- which represents 20 percent of that ceiling plus a $60 deductible charge.

The remaining $930.50 is a paper number, in a sense, that Dr. Matory in effect writes off since he cannot collect it immediately from Medicare and does not as a rule attempt to collect it from the patient. But that extra $930.50 is important because, as a part of Matory's $2,000 total charge, it increases the base that Medicare will use for making reimbursements to him in the future. It also ensures that his personal ceiling for reimbursement will be at the areawide peak.Moreover, the total $2,000 fee is fed into the computer that calculates the base on which all area physicians are reimbursed by both Medicare and non-Medicare insurance programs.

If Dr. Matory charges less than $2,000, the base for his future reimbursements will be smaller and his potential income reduced. Medicare reimburses doctors based on a history of their fees and on fees for the area in which they practice. Lower fees mean lower reimbursement.

"My position is to take the Medicare [payment] -- which is best for the patient -- and then increase the fee to build a profile that will lead to higher payments." Matory said.

Raising fees to increase the base is offset somewhat by Medicare's policy of limiting reimbursement increases to about 8 percent a year for an area. There is no limit on increases by non-Medicare insurance carriers.

Matory said his experience tells him that the Medicare structure "isn't really working for the patient or the doctor." He said that the Medicare approach "seems to be to pay the least out of their cash that they can. . . . This is why some physicians won't accept the Medicare reimbursement [and bill their patients for the difference between their fees and the program ceiling payment]."

Matory said he does not ask his Medicare patients to pay the difference.

The Medicare guidebook, released yesterday by the Public Citizen Health Research Group, includes a series of charts listing area doctors with five medical specialties, their fees for certain medical procedures and indications of whether they accept Medicare reimbursement as payment in full.

Several physicians cited in the directory criticized the methods used by the Nader Research Group and questioned the accuracy of some of the fees listed.

"He [Nader] is comparing us to old inadequate data; he is a rabble-rouser," said Dr. J. W. Canter, a Washington surgeon.

He said he and his partner, Dr. R. L. Flax, charge fees that are appropriate to the difficulty of the procedure and that are customary for this area. Canter said that the directory "implies that we are overcharging because we are over the Medicare level . . . but in fact the Medicare fee data is three years old . . . and inflation affects all of us."

Dan Sigelman, who wrote the report, said the Medicare repayment data goes back a maximum of 18 months.

Canter also said that the comparison of physicians' customary charges to area Medicare ceilings is meaningless when the physicians accept the Medicare assignment of benefits and do not bill patients for the difference between the fee and the ceiling.

Some other physicians called yesterday disagreed with the fees listed in the directory as their 1978 customary fee for a variety of medical procedures, ranging from gall bladder surgery to hernia repair.

The customary charge listed for gall bladder surgery by Dr. Elie A. Sayan, a Maryland physician, is listed in the book as $1,025 for 1978. That was $440.30 over the ceiling allowed by Medicare for that year.

But Sayan said, "That is wrong. My current charge is $700 to $800. No extra charges for complications. I don't know where they got that number."

Sigelman said the numbers came from Medicare records of payments by area physicians, including Sayan. The charges were obtained under Freedom of Information laws, he said.