President Carter and Defense Secretary Harold Brown have sent extraordinary letters to the Senate warning that billions the House just added to the Pentagon budget for weapons would hurt rather than help national defense.

Carter wrote Chairman John C. Stennis (D-Miss.) of the Senate Armed Services Committee that the extra $6.2 billion the House approved on Wednesday skews the defense budget and "could adversely affect today's military readiness. . . ."

Brown in a separate letter to Stennis, attacked the House additions as "a serious misallocation" that "places undue stress on our scarce economic resources and, ironically, jeopardizes the added military capability we all seek."

The House action Wednesday was another in an unbroken string of pro-defense votes in the Capitol in recent months. The Carter-Brown letters represent one of the few instances the administration has resisted and argued for restraint.

The president and defense secretary contend the House-passed defense increases, in just the research and procurement accounts of the Pentagon budget, threaten to crumple their whole blueprint for the national budget, which next year Carter wants balanced.

They go beyond expressing that general concern, one that will take front the center in the argument over federal spending ceilings just set in a House-Senate budget conference, and fire at specific additions for weaponry.

"These increases," wrote Carter of the House decision to push the weapons procurement budget from the requested $46.9 billion up to $53.1 billion in fiscal 1981, "will make it most difficult for the Appropriations Committee to structure a 1981 defense appropriations bill consistent with a balanced budget without severe reductions in operations and personnel areas critical to the readiness and capability of our forces."

The $6.2 billion addition, continued Carter, "could adversely affect today's military readiness by forcing offsetting reductions in the operations and personnel accounts later in the congressional process.

"I urge you," said Carter to Stennis, "to give particular attention to the priority needs of the operations and personnel accounts in the defense budget and to the nation's overall budgetary objectives."

The president wrote that "I am particularly concerned" about the $600 million the House added to transform the B1 bomber, which Carter shot down in 1977, into a flying platform for launching cruise missiles in the 1980s and 1990s.

Existing B52 bombers can do that job for years to come, said Carter, and building "a second, extremely costly cruise missile platform is both premature and unneccessarily expensive."

He said he was equally concerned about the House authorization of $560 million to bring the World War II air-craft carrier Oriskany and battleship New Jersey out of mothballs.

"Because they require thousands of new crew members," Carter wrote, "both of these ships would aggravate current Navy ship manning problems. Even if we could overcome these constraints, it remains inefficient to apply hundreds of millions of dollars to resurrect 1940s' technologies for only a few short years of stretched operation."

The $492 million the House added to buy an extra 24 Navy F18 war-planes "would likely" cut into the money needed to repair and fly the aircraft the Navy already has, Carter continued.

And it makes no sense, the president said, to spend the $907 million the House added to help buy two more Los Angeles-class attack submarines when "we plan to design a new class of submarine." This puts Carter at odds with his old mentor, Adm. H. G. Rickover, who has been urging Congress to reject the Pentagon's plan to build something simpler and cheaper than the $600-million-a-copy Los Angeles sub.

In what one Veteran staffer called "an extraordinary if not unprecedented intrusion" into the legislative process by a president, Carter sent his letter to Stennis on May 15 when the House was just starting to debate the 30 percent increase in weapons' money.

As it turned out, the president's opposition might have made it more difficult for some Republicans to oppose the budget-busting bill for fear of being accused of being allied with Carter. The bill passed Wednesday night 338 to 62 with no serious challenge to the total authorized, as distinguished from individual weapons.

Brown wrote Stennis May 20 that "however appealing" extra money for the Pentagon may appear, "funding for defense cannot be looked at in isolation. It must be balanced with non-defense funding requirements and with the need for fiscal responsibility.

"Substantial additions," Brown cautioned, "would skew that because . . . it is not a prudent use of resources in fiscal 1981, much less in years to come, to accept the very large increases proposed by the House."

In objecting to the specific House additions for ships and aircraft, Brown contended they would upset the president's "careful balance of efficient procurement levels on one hand and our competing military and domestic needs on the other. . . ."

In addition to the weapons additions protested by Carter, Brown pleaded with Stennis to restore the cuts the House made in Pentagon money requests for the Roland anti-aircraft missile and the stockpile of weapons for sale abroad.

The Senate Armed Services Committee is still marking up its version of the weapons authorization bill. In a separate legislative process, the House and Senate will decide later how much of the money authorized should actually be appropriated to the Pentagon.

A House-Senate conference on Wednesday agreed on high money ceilings for national defense in fiscal 1981 through 1983. These ceilings are overall targets for total military spending, not allocations to specific research and weapons.