A senior House Armed Services Committee staff aide, in a parting salvo before leaving his job, declared yesterday that the Navy should scuttle its planned Seawolf attack submarine to build a better boat, and sink its two aircraft carriers on the drawing board to hold down the Defense Department budget.

Anthony R. Battista, who, for the last 14 years has often infuriated generals and admirals by poking holes in their pet projects as staff director of the research and development subcommittee, said on the eve of leaving his post next month to become a private consultant that the Pentagon must take drastic actions now to keep its budget from ballooning out of control in the 1990s.

If Defense Secretary Frank C. Carlucci canceled some big weapons programs and got really tough on research projects, Battista said, he would not have to take thousands of soldiers, sailors and airmen off the payroll to accommodate the cuts Congress is almost certain to make in the next five fiscal years, just as it has for the last two.

The SSN21 Seawolf submarine now entering development is not good enough to combat the undersea threat posed by rapid Soviet advances, Battista said. The Soviet Akula attack submarine "is the best submarine in the world today," he said. Last year Battista took the lead in persuading the House research subcommittee to cancel the Seawolf and strive for a better submarine. Congress reversed that decision and funded the Seawolf as well as providing $100 million to work on a more advanced attack sub.

The Navy wants $1.7 billion in the fiscal 1989 budget to buy the first Seawolf. Carlucci is reviewing that and other plans in his effort to restructure his budget to fit the new realities of a Congress determined to flatten the Defense Department's spending rather than increase it yearly as President Reagan had requested.

Congress last year approved a $3.3 billion nuclear-powered aircraft carrier, due in 1997, and a $3.6 billion carrier, for service in 1999.

"We can fix the surface Navy," Battista said in making his case against the two new carriers. "The real threat is undersea," he said, meaning that developing better submarines and combatting Soviet ones should receive top priority in the era of tighter budgets.

Service leaders contend the Navy is confronted with many carriers growing old simultaneously and must build new ones to have 15 capable of being deployed to distant locations. They also insist that the Seawolf will be the best attack submarine.

In other remarks made during a luncheon with a group of reporters, Battista discussed:

Procurement. The elaborate rules that Congress and the Pentagon have imposed on defense contractors have cluttered the process to the point that the nation is now "spending $10 to save $1." A better approach would have been to make the punishment for shoddy work and outright fraud so severe that few contractors would have dared take the risk.

Air Force Maverick air-to-ground missile. Not worth continuing to buy.

Research duplication. The Pentagon has been so lax in winnowing out duplicative projects that the military services currently are developing six different radio programs "all to communicate with another airplane."

Navy shipbuilding. The fragility of the USS Stark, severely damaged by a French Exocet missile in a Persian Gulf attack last year in which 37 sailors died, and problems with the new Arleigh Burke destroyer stem in part from "incompetence" in designing ships. "We're running out of naval architects."

Battista plans to leave his subcommittee staff post on Feb. 15. He will be succeeded by Carl T. Bayer, who is another subcommittee staff aide, and a new staff member, Thomas Hahn, who formerly worked there before going into private business.