President Reagan used his annual budget message to urge Congress to pass the Senate's phased-in version of legislation to provide catastrophic-care coverage under Medicare, rather than a rival House bill.

There is no mention in the budget, however, of either of the other two prongs of the three-part program proposed by Health and Human Services Secretary Otis Bowen, M.D., to deal with the costs of catastrophic illness.The budget does not include any such new initiatives to deal with catastrophic illness for the non-elderly or disabled population or to create a program to provide insurance against the costs of long-term care.

The administration remains committed to the enactment of legislation providing affordable acute-care catastrophic illness protection and outpatient prescription drug coverage for our nation's elderly and disabled, the president said.

Such legislation must be deficit neutral, with benefits paid from newly created self-financed trust funds, the president added.

The budget message is a shift from earlier attempts by the administration to keep the program small and not include prescription drugs.

The Health Insurance Association of America put the best light possible on this presidential support for a program designed by congressmen to replace Medigap insurance, which fills in the gaps in Medicare benefits.

Spokesman Benno Isaacs says insurers believe there will still be a need for supplemental policies to fill in gaps due to balanced billing in which physicians charge higher fees than Medicare allows; to deductibles for initial hospital stays and to the absence of coverage for dental care and eye glasses.

Supplemental policies, he said, will be changed to offer those benefits rather than those now covered that would be taken over by the government program.

Both the House and Senate have passed different versions of catastrophic insurance for the elderly, with both bills differing from less extensive programs recommended by President Reagan last year.

The president used his budget message to attempt to influence conferees toward the Senate plan.

The Senate-passed version of H.R. 2470, the Medicare Catastrophic Protection Act, is consistent with the administration's principles for an acceptable catastrophic health insurance bill, the president said.

The Senate version sets an annual limit of $1,850 on out-of-pocket expenses incurred for Medicare-covered expenses. Additionally, 80 percent of prescription drug costs exceeding $600 annually would be covered by the program.

The prescription drug coverage in the Senate bill was to be phased in with full coverage available Jan. 1, 1993. Since the program was not enacted in 1987, the budget message said administration support assumes modifications in effective dates . . . .

The Senate version includes administration demands that financing of the prescription drug benefit be included in a separate trust fund so there would be no cross-subsidies between medical care and drug benefits.

The benefits would be financed from a supplemental premium of $1.08 a month for every $150 in federal income tax liability up to a ceiling set at $800 for 1988 and rising to $1,000 in 1992. This premium would be per Medicare enrollee, not per family.

Premiums for pharmaceutical coverage would be $2 a month in 1991, $3.50 in 1992 and $4.80 in 1993.

The House bill limits out-of-pocket Medicare approved costs to $1,623 and would cover 80 percent of prescription drug costs over $500 annually.

The House version is financed by an income-based premium that would charge $580 a person in additional taxes the first year to individuals with incomes of $20,000 or more.

In contrast, the Senate bill is based on an estimate that an elderly family would have to have income exceeding $100,000 annually to reach the $1,000-per-person cap in that bill.

The House pharmaceutical benefit, which does not contain the long Senate phase-in, would charge an additional Medicare premium of $2.60 in 1989, rising to $5.50 by 1992.