Ambassador Alfred L. Atherton, in a change of plans, probably will skip Israel on his now mediation mission to the Middle East, State Department sources said yesterday.

Officially, spokesman Tom Reston said the Israeli visit of the U.S. emissary, who left Washington Tuesday night, is "up in the air." Reston said Atherton's plans depend on those of Israeli Foreign Minister Moshe Dayan. Who has been seeking an early meeting in Washington with Secretary of State Cyrus R. Vance.

State Department and Isaeli sources said last night that Dayan probably will come to Washington in the middle of next week. Vance is due back from an Africa-Moscow journey Monday.

Israel has been unenthusiastic about Atherton's go-between role in recent Middle East diplomacy, preferring to proceed instead in direct Jerusalem-Cairo talks.

However, contacts between the two capitals at a high level, most recently between Egyptian President Anwar Sadat and Israeli Defense Minister Ezer Weizman, are now in abeyance.

The Israeli government also is reported to be anxious to keep its negotiations with the United STATES ON THE FOREIGN MINISTER LEVEL Ezer Weizman, are now in abeyance.

The Israeli government also is reported to be anxious to keep its negotiations with the United States on the foreign minister level if possible.

Thus Dayan-Vance meetings here would be preferred to Dayan-Atherton meetings in Jerusalem, in this view, meetings here would be preferred to Dayan-Atherton meetings in Jerusalem, in this view.

The Tel Aviv newspaper Ha'aretz reported Monday that Dayan and Prime Minister Menachem Begin rejected a U.S. proposal to renew Atherton's mediation efforts. The newspaper reported that they cited "Egyptian intransigence" as well as U.S. support of Egyptian positions as reasons for disapproving Atherton's mission.

Israeli officials here and in Jeruselem denied the newspaper account. They attributed the change in Atherton's plans to a conflict with the Dayan trip.

Atherton was in London yesterday en route to Cairo meetings scheduled to begin at the end of this week.