The Clinton administration hopes to have an agreement with Russia by next June on modification of the 1972 Anti-Ballistic Missile Treaty that would permit the United States to go ahead with a limited national missile defense system, a senior State Department official said yesterday.

John D. Holum, President Clinton's nominee to be undersecretary of state for arms control and international security affairs, told a Senate Foreign Relations subcommittee that "sometime in the next weeks or perhaps months," the Pentagon will decide what a national missile defense against a limited attack would look like.

Once that decision on the "architecture" is made, Holum said, "Our intention is to complete an agreement on permitted national missile defense . . . by next June, when there would be a deployment decision" by Clinton.

Holum added: "It's important that the decision on architecture will be made based on the threat, based on security considerations. Then we'll decide what amendments to the treaty are needed and how to approach the treaty. We're not saying protect the treaty, so tailor the defense to fit the treaty."

The schedule could slip, a White House spokesman said yesterday, because the Pentagon wants to complete four tests before making its recommendation to the president.

At their recent meeting in Cologne, Clinton and Russian President Boris Yeltsin agreed that later this summer a U.S. team would present to Russia the modifications to the ABM treaty needed to permit the proposed system.

Holum, who headed the Arms Control and Disarmament Agency for six years before it was merged into the State Department, said he believed that no matter what the proposed U.S. missile defense system looked like, it would require ABM treaty changes.

Holum also said the system's architecture "should be geared toward the threat, also geared toward the technology that we have available to meet the threat . . . [and] based very heavily, obviously, on the recommendations of the Department of Defense and the Joint Chiefs on what they feel will be an effective defense."

Responding to a question submitted by committee Chairman Jesse Helms (R-N.C.), Holum said he thought the administration would delay submitting to the Senate for approval 1997 amendments to the ABM treaty agreed to by Clinton and Yeltsin.