The United States and the Soviet Union agreed yesterday to a two-week delay in high-level nuclear arms control negotiations, with "substantial difficulties" blocking a new accord.

That decision wiped out a long-scheduled negotiating session between Secretary of State Cyrus R. Vance and Soviet Foreign Minister Andrei A. Gromyko planned for Sept. 7-9 in Vienna.

Gromyko is now scheduled to meet in Washington on Sept. 22-23 with Vance, and probably President Carter and other senior officials, followed by additional talks with Vance in New York later in September or early October.

This delay will allow time "to lay a better groundwork, we hope," for overcoming obstacles to a new accord in the strategic arms limitation talks (SALT), said State Department spokesman Hodding Carter III.

The spokesman minimized the cancellation of the Vienna talks, which was describe officially as an agreement "to defer" them. As Gromyko was coming to the United States anyway for the United Nations General Assembly session, Carter said, "Both sides felt that nothing would be lost and there could be some advantage in waiting for the "genuine progress" and increased "understanding" between the two sides in their continuing lower-level nuclear arms negotiations in Geneva since May, the spokesman said. Carter said there were also "genuine scheduling difficulties" about the Vienna meeting, since Vance's presence in Washington is desired for the Sept. 7 signing of the Panama Canal treaties by up to 20 Latin American heads of state or foreign ministers.

But the core of the problem, Carter acknowledged, is that the two sides are at odds on the central obstacles which have blocked a SALT agreement since the Carter administration took office.

As the spokesman expressed it with diplomatic nicety, the same "exchanges" since May which produced "a better mutual understanding . . . also showed that substantial difficulties remained to be overcome."

He listed four areas of unresolved issues.

Other sources put it much more bluntly. They said talks at the White House last week with Soviet Ambassador Anatoliy F. Dobrynin showed no prospect for resolving any basic differences in Vienna. As a result, when Vance returned from Peking over the weekend, it was decided in talks with President Carter to ask the Russians to scrap the Vienna session.

State Department spokesman Carter indicated there is no great concern by either side that the present temporary limit on offensive strategic weapons, signed in 1972 by Soviet leader Leonid I. Brezhnev and President Nixon, expires Oct. 3.

"We are exploring with the Soviets ways to handle that problem and we are and will be consulting with Congress on the subject," the spokesman said. President Carter, he noted, has repeatedly said he places no "arbitrary deadline" on the negotiations, and has said that the Oct. 3 date can be extended.

The administration hopes to induce Congress to forgo a public inquiry, or legislation, on an extension.Congressional attitudes can be affected by the extent of internal U.S. differences on negotiating tactics that are known to exist among the principal agencies - the National Security Council, State and Defense, departments and the Arms Control and Disarmament Agency.

The spokesman brushed off reporters' questions yesterday about differences inside the administration, saying they were "not a major component" of the decision to bypass the Vienna negotiating round.

He said "the primary unresolved issues" now blocking agreement are, in the jargon of the nuclear negotiators: "Cruise missile limitation, constraints on the modernization of strategic systems, limitations on the Soviet Backfire bomber, and a number of more technical items related to verification."

What this translates into, in laymen's terms, is that the Soviet Union is insisting on tight limits on the American air-launched, long-range cruise missile, similar to an unmanned jet plane with a nuclear warhead. Since President Carter's decision against producing B-1 bombers, the relatively inexpensive cruise missiles have become an additionally important American weapon, to be launched from older B-52 bombers, or even from jet airliners.

Additionally, the United States seeks limitations on the large Soviet heavy missiles known as SS-18, which President Carter said causes the United States "great concern." The Soviet Union is strenuously balking at this demand. The United States also seeks assurances that the Soviet bomber known as Backfire cannot be used as an intercontinental weapon.