The first time "not in my backyard" protest against the MX missile system arose in Congress yesterday and was promptly crushed by the House.

Rep. Jim Santini (D-Nev.), his state's lone congressman, told the chamber that the Air Force, with President Carter's backing, wants to put 70 percent of the MX system in Navada and the rest in Utah.

He worried that there will not be enough water to supply the large work force needed to construct the system, and sought to disperse the system over several states. His effort came as the House continued debate on a bill authorizing $42 billion for weapons.

Also during the debate, the House beat down an effort to delete funds for a nuclear aircraft carrier. President Carter opposes the carrier so strongly that he vetoed last year's procurement because it included money for the $2 billion ship.

By 286 to 112, the House rejected an amendment by Rep. Ronald V. Dellums (D-Calif.) who calls the carrier a sitting duck in the nuclear age. The House also voted down 309 to 96 an amendment by Rep. Vic Fazio (D-Calif.) to authorize money for an oilfired, Kennedy-class carrier rather than fund another nuclear-powered Nimitz carrier.

While the fight over a nuclear carrier is a perennial one, yesterday marked the first time that the MX system has come under challenge in Congress. The deployment scheme calls for hauling giant missiles from one study garage to another spread in a racetrack pattern at the bottom of deep valleys in Navada and Utah. The cost is estimated at between $30 billion and $40 billion.

Santini said that construction would overwhelm sparsely populated Navada, which is already short on water.

"They're talking about 22,000 to 30,000 employes" building the MX racetrack "in an area of 7,000 people. Where's the water going to come from?"

Santini, urged that the racetracks be built on government land in Nevada, Utah, Arizona and New Mexico.

Chairman Melvin R. Price (D-Ill.) of the House Armed Services Committee read a letter from Republican Gov. Robert List of Nevada welcoming the MX into the state.

Nevada's two senators, Democrat Howard W. Cannon and Republican Paul Laxalt, are divided on the MX, with Cannon endorsing it and Laxalt seeking assurances the system would not lock up too much land in the state.

Rep. Richard H. Ichord (D-Mo.) warned his colleagues that spreading the MX among four states would push the cost of the system "through the roof."

Price linked the MX with Senate ratification of the pending strategic arms limitations treaty, delcaring: "It's foolish to think we're going to get a SALT treaty passed" without going ahead with the new land-based missile.

Santini's amendment was voted down 289 to 84 in one of several expressions of strong House support for the MX.

Another MX amendment, sponsored by Dellums, called for deleting money for the missile from the procurement bill on the grounds it was really a first strike weapon that would put a hair trigger on nuclear warfare. Dellums' amendment was defeated 305 to 86.

Since the Senate has already rejected building another nuclear aircraft carrier in passing its own defense procurement bill, the issue will be resolved in a House-Senate conference.Veteran House staffers said yesterday that the overwhelming votes against removing the nuclear carrier from the House bill would make it hard to budge on the issue in conference.

Defense Secretary Harold Brown sent a letter to the House as a procurement bill was being debated in which he declared the Carter administration still opposed the Nimitz nuclear carrier but would settle for building one of the Kennedy class, despite Carter's assertion of last year in his veto message that he favored a smaller carrier than the Kennedy.