Eugene V. Rostow, director of the U.S. Arms Control and Disarmament Agency, said yesterday that Secretary of State George P. Shultz has found "no substance" to allegations that Rostow and veteran negotiator Paul Nitze went beyond their instructions in negotiating with the Soviet Union.

The accusations are an example of "the favorite Washington sport of shooting at public officials from ambush," Rostow told participants in a conference on "Defense in the l980s" at the Capital Hilton hotel.

The Washington Post reported on Sunday that presidential national security adviser William P. Clark relayed charges to Shultz that Rostow and Nitze exceeded their authority in arms control discussions with Soviet officials. Rostow's critics in Congress first leaked the accusations in a continuing fight over the blocked confirmation of two senior officials in Rostow's agency, Robert Grey and Norman Terrell.

"There were of course some charges of this sort," Rostow said yesterday in referring obliquely to the accusations against him and Nitze. Rostow refused to be any more specific about the charges aimed at him and Nitze, who leads the U.S. negotiating team on limiting European-based nuclear missiles, on grounds that they involve unwarranted allegations about sensitive matters.

When this matter was "brought to Judge Clark's attention," Rostow said, "he naturally asked Secretary of State Shultz to take a look" at the accusations. "Secretary Shultz," Rostow said, "found no substance in these charges," and "the matter is satisfactorily closed."

Officials at the State Department and the White House had considered issuing a joint commentary on the episode along with the arms control agency, but they declined yesterday to discuss Clark's memo to Shultz, or Shultz' reaction to it. When asked if Shultz agrees with Rostow's account, a State Department spokesman said only that "We don't comment as a matter of practice on allegedly leaked documents."

Rostow's own future as director of ACDA has been cast in doubt in the dispute between him and conservatives in Congress led by Sen. Jesse Helms (R-N.C.), in which both sides privately concede that Rostow subordinates Grey and Terrell are only the ostensible targets. The core of the dispute is the conservatives' charge that the Reagan administration, like its predecessors, has failed to indict the Soviet Union for alleged gross violations of all past arms control accords.

Rostow reiterated yesterday that all accusations against Grey and Terrell "have been fully and patiently investigated" and "are without substance." Their nominations by the president, he said, "should be upheld by the Senate," and Rostow expressed confidence that this issue will be "satisfactorily resolved during this month." As for himself, Rostow said, "The president gave me this post to do a serious job of arms control," and "I plan to continue pursuing President Reagan's mandate vigorously and to explore every avenue leading towards meaningful arms control. . . ."

Other sources, however, have said that the White House is unwilling to spend further political capital on pursuing the dispute with Helms and other conservatives who share his views. Rostow is expected to meet with White House officials this week, associates said. Rostow is also seeking another meeting with Helms, with whom he has met in the past without success.