Soviet concern that American-built cruise missiles might be deployed in Europe and West Germany's acknowledged interest in these new weapons are two factors that help explain why Moscow yesterday sharply rejected U.S. proposals for a new strategic arms agreement.

The cruise missile is a small, relatively inexpensive, pilotless jet aircraft that can carry an atomic bomb or conventional explosive over long distances with considerable accuracy.

The United States has a long lead over the Soviets in the ability to design and build these weapons. The cruise missile has been at the heart of the superpower dispute over the future course of arms limitation agreements for almost two years, but it was not included in either of two U.S. arms limitation proposals made in Moscow this week.

Although the Soviets are most concerned about long-range cruise missiles fired from U.S. bombers, ships or submarines, they are also said to fear that short-range missiles could be installed on land, in trucks or in a wider array of smaller allied attack planes here and elsewhere in Europe.

This would, for example, greatly increase the striking power of these more numerous aircraft, giving them the ability to lob missiles at targets deep inside East Europe or the Soviet Union.

Many West German defense specialists have indicated private fascination with the new technology as a way for their own forces, as well as for the rest of NATO, to help offset the numerical superiority of Warsaw Pact land and air power.

Although the West Germans do not have nuclear weapons, the expected high accuracy of the cruise missile gives it the potential to knock out distant targets using conventional explosives.

The keen interest here in preserving this weapon as an allied counter to Soviet advantages helps explain why the U.S.-Soviet disagreement in Moscow this week over a new agreement has not upset some defense officials here. The Kremlin is demanding that the cruise missiles be covered in any new arms limitations.

On the other hand, some officials feel that the West German interest in cruise missiles may be shortsighted. Even if the United States leads now, they argue, the Soviets might eventually catch up and these weapons would only reinforce the likelihood that any future war would be fought largely on a German battlefield, something the Germans would like to avoid.

Despite the Bonn Defense Ministry's interest in the cruise missile, however, the failure of the U.S. mission to Moscow this week is causing concern for West German Chancellor Helmut Schmidt.

Schmidt appeared at a press conference here today with Secretary of State Cyrus R. Vance after the two leaders met for more than four hours in the aftermath of Vance's mission to Moscow.

Schmidt tried to put an optimistic assessment on the Vance mission, but his aides said privately that the chancellor was disappointed.

Schmidt said that as he interpreted the outcome, neither the United States nor the Soviets felt that they were "at the end of the road yet" on the negotiations.

"I continue to believe that the basic interest of the U.S., the Western world as a whole, and the Soviet Union, reflects a very strong desire to arrive at a SALT II agreement. One could not expect a first meeting of this kind," Schmidt said, "to produce tangible results."

Schmidt has aligned himself closely with U.S. efforts toward detente, however, and any arsurgence of superpower confrontation could hurt him and probably West Germany.

Schmidt also is anxious for progress in the East-West troop reduction talks that, like the nuclear arms talks, have been stalled for some two years. It is clear, he said, that no progress will be made in those efforts to reduce tensions in Central Europe until there is progress in the nuclear arms negotiations.

Schmidt had planned to try to bolster his sagging political fortunes here with a new burst of foreign policy initiatives this year, including playing an important role in the troop-cut talks. But if relations between Moscow and Washington continue to sour, he will have a hard time carrying through such plans.

Thus, while attention remains focused on the two superpowers, the effect of their new disputes under the Carter administration is having a widening effect.