Secretary of State Cyrus Vance arrived in the Middle East tonight to open the next round of Egyptian-Israeli negotiations, but his call for "a new era of peace" was clouded by a dispute about opening the borders between the two countries.

In talks with Vance earlier today in London, Israel Prime Minister Menachem Begin is known to have expressed concern that Egyptian President Anwar Sadat intends to go back on what Israel claims was a promise to open the borders permanently on Sunday.

Begin contends Sadat made the promise last April during Begin's visit to Cairo. The peace treaty calls for normal border crossings only nine months after Israel finishes the next stage of its withdrawal from the Sinai, but Begin says Sadat agreed to speed the timetable, as a gesture of good faith.

Sadat, who met with Vance here tohight, told reporters he had made a promise to Begin but, pressed to explain the promise, Sadat chuckled and said: "Why don't we wait until Sunday?"

The two leaders will meet with Vance on Sunday at El Arish in the Sinai Peninsula to mark formally the return of the town to Egypt, which occurs Friday in a ow-key military turnover ending 12 years under Israeli occupation. Vance also will be present Friday at the Israeli town of Beersheba when delegations from the two countries formally open the next phase of their peace negotiations.

In what was viewed as a possible forecast of difficult days ahead, defiant Jewish settlers on a farm near El Arish sprayed insecticide and threw stones and vegetables at Israeli soldiers trying to evict them on the eve of the turnover. The 200 angry settlers relented and moved out of their 10 acre vegetable patch after clashes in which several soldiers and farmers were injured.

Also underlining obstacles to be overcome in the next phase of negotiations, Palestinian guerrillas shelled a northern Israeli town and, hours later, Israeli jets bombed Palestinian bases deep inside Lebanon for the second straight day. The guerrillas have vowed to increase terrorist activity to undermine the Egyptian-Israeli peace treaty and frustrate the Beersheba talks opening Friday on autonomy for Palestinian inhabitants of the Israeli-occupied West Bank and Gaza.

These new talks are expected to be even more agonizing and time-consuming than the months of top-level negotiation required to produce the Egyptian-Israeli peace treaty signed last March.

Israel, concerned about its security, is reluctant to allow any governmental mechanism in these areas that might be turned, into an independant Palestinian state. But Sadat, whose treaty with Israel has caused Egypt to be shunned by its traditional Arab allies, is under great pressure to prove that his approach offers the best hope of solving the Palestinian problem.

The Carter administration, eager to help Sadat regain his influence in Arab circles, wants the negotiations to project what one U. S. officialal in Vance's party called "an impression that serious talks are going on." While conceding it is likely to take months before the talks show signs of headway, U.S. officials keep stressing the need to avoid undue delays and disputes over side issues.

That is why the argument over open borders has proved worrisome to U.S. mediators. Under the Egyptian-Israeli peace agreement, borders between the two countries are to be opened to normal traffic at the end of nine months following completion of a parial Israeli withdrawal from the Sinai.

However, when Begin visited Sadat in Cairo in April, he announced publicly that Sadat promised to expedite the process and open the borders at the time of the El Arish turnover. Yesterday, though, Begin, who is on a visit to London, said there that Egypt had informed Israel it was changing its mind and returning to the original nine-month timetable.

It is generally believed here that Sadat has been greatly disturbed by the unexpected vehemence of Arab world efforts to punish and isolate him and has had second thoughts about taking steps at this time that would further antagonize such key former supporters as Saudi Arabia. For that reason, he is belived to be aiming at talking Begin into delaying such gestures as an expedited opening of borders or exchange of ambassadors.

In attending the ceremonies at El Arish and Beersheba, Vance hopes to demonstrate the continuing priority that the United States places on furthering the Middle East peace process. In particular, he is known to be sending a signal by his presence that the appointment of presidential trouble shooter Robert Strauss at the new U.S. mediator for the talks does not mean any lessening of his own or President Carter's interest.

That was the note he tried to strike when, following his talks with Sadat, he said: "It is paricularly joyful for me to be here when tomorrow El Arish is to be returned to the Egyptian nation . . .There are many obstacles ahead, but with the return of El Arish and the negotiations that begin tomorrow, we will be moving toward a new era of peace." CAPTION: Picture, Israeli Prime Minister Menachem Begin hugs Secretary of State Cyrus Vance. UPI