Health and Human Services Secretary Margaret H. Heckler yesterday proposed reimbursement rates that are higher than many had expected for the new Medicare hospice program.

Leaders of the National Hospice Organization said the rates, which have been the subject of controversy for months, were in general "a substantial improvement over those proposed earlier" by some HHS officials.

Last year, Congress authorized Medicare to pay benefits for hospice services starting this November. Under the program, terminally ill people who are thought to have only six months to live can choose to remain at home, but receive counseling and medical care financed by Medicare and supervised by a hospice organization.

The patients still would be eligible for some hospital services. Under the proposed regulations, the government would pay $53.17 for each day the patient is at home under hospice supervision.

Where intensive home care requiring nursing is needed, the rate would be $155.98 for eight to 16 hours, $233.97 for 16 to 20 hours, and $285.96 for 20 to 25 hours.

For care in an inpatient facility to provide a brief rest for relatives who are caring for the person at home, Heckler set a rate of $61.65 per day.

When the patient must go to the hospital either because he is experiencing great pain or has acute symptoms, HHS would pay a single flat rate of $271 per day. HHS initially had proposed a far lower rate for general inpatient care for pain control, about $60, but the final single rate for both pain and acute symptoms was "much more appropriate," hospice spokesmen said.

The payments would be made to the hospice, which would pay the hospitals and nurses.

Heckler said that as soon as President Reagan signs recent legislation capping the average total payment a hospice could receive at $6,500 per patient, she formally will impose that cap instead of an earlier one of $4,232.