A senior Israeli defense official charged today that the United States has impeded the Lebanon troop withdrawal negotiations by giving Lebanese President Amin Gemayel the impression that he does not have to cooperate with Israel on security arrangements in southern Lebanon.

The official, who is among the most influential members of Prime Minister Menachem Begin's government, declined to be identified. He made the charge to American reporters traveling with Secretary of State George P. Shultz on his shuttle effort to work out a Lebanon troop withdrawal accord.

The charges introduced a jarring note into the atmosphere of cordiality that has surrounded Shultz since he arrived here Wednesday to begin shuttling between Jerusalem and Beirut.

State Department spokesman John Hughes, asked for comment on the charge, said, "That certainly isn't the United States' or the secretary of state's view of President Gemayel's intentions."

Instead, Hughes asserted, Shultz has found in his talks here and in Beirut that both the Israeli and Lebanese governments appear eager for an accord that will pave the way for the withdrawal of Israeli and other foreign forces from Lebanon.

But Hughes also reiterated the U.S. position that an agreement should not allow Israel to retain any residual military presence in southern Lebanon. He also stressed anew the U.S. position that the Lebanese Army is capable of maintaining a southern Lebanon security zone in a manner that will protect Israel's northern border from terrorist attacks.

These were the U.S. positions that the senior Israeli official complained about at a luncheon given for the visiting American press. He charged that the Reagan administration, whether intentionally or not, "has played a less-than-positive role" by leading Gemayel to believe that he can rely on American forces in Lebanon and American training of the Lebanese Army to solve his security problems.

Israel, in a position supported by Defense Minister Moshe Arens, has insisted that security arrangements for southern Lebanon should include joint Israeli-Lebanese patrols, Israeli liaison officers and "logistics centers" inside Lebanon and the assignment of principal responsibility for the region to the Christian militia forces of Saad Haddad, a cashiered Lebanese Army major allied with Israel.

Lebanon has objected to most of these demands as a violation of its sovereignty. The United States, which is anxious to help Gemayel assert his authority over his badly divided country, has supported the Lebanese arguments.

The reasons for the Israeli official's charges at this time were not immediately clear. They appeared to be a new effort to influence the U.S. government and public opinion into dropping some of its opposition to the Israeli security demands.

A similar effort was made in March by Israeli Foreign Minister Yitzhak Shamir, who visited Washington in an attempt to appeal to Shultz over the head of Reagan's special Middle East envoy, Philip C. Habib. But Shultz rebuffed that attempt by replying that Lebanon is capable of dealing with terrorist activity on its side of the border.

Hughes said today that there "never has been any suggestion or serious discussion" of the idea that U.S. Marines, now stationed around Beirut as part of a multinational peace-keeping force, might be moved to southern Lebanon "to fulfill a security role." He stressed, though, that U.S. training of Lebanese forces will continue.

Despite the stir caused by the Israeli official's remarks, both U.S. and Israeli officials said today's talks between Shultz and Begin had proceeded in a cordial and positive manner. But they also warned anew that it will take some time to tell whether an agreement is possible.

In private, officials on both sides said Shultz had reported to the Israelis on his meetings Thursday in Beirut and that several ideas "for clearing up misconceptions" had been discussed so that Shultz can take them back to Beirut for further talks on Saturday.

[At least one Israeli soldier was killed south of Beirut today, United Press International reported. Witnesses said two Israeli soldiers were killed in an ambush but an Israeli military spokesman said one soldier was killed and three wounded.]