The top Israeli and Egyptian negotiators in the Middle East talks met jointly with Secretary of State Cyrus R. Vance yesterday, but informed sources said major differences still remain over the final form of a peace treaty between the two countries.

The Blair House meeting, mediated by Vance, concentrated on trying to reconcile the conflicting changes that the Egyptian and Israeli governments want made in the draft treaty tentatively agreed on by the negotiators here 11 days ago.

According to the sources, the dominant issue still clouding the talks is disagreement over language on the treaty that would establish a link between an Egyptian-Israeli peace and future efforts to resolve the status of the Israeli-occupied West Bank and Gaza Strip and their Palestinian inhabitants.

Egypt, which is sensitive to concern within the Arab world about the Palestinians, wants the linkage to be as explicit as possible. But Israel seeks to weaken the linkage language to bolster its contention that there is no legal tie between the two issues.

The dispute was heightened last week by Israel's announced intention to expand its existing settlements on the West Bank. That move angered both Egypt and the United States because they fear it could make more difficult the effort to achieve a comprehensive Middle East peace involving the other Arab countries.

The meeting yesterday represented an attempt by all three countries to keep the problem of West Bank settlements from impeding the talks. But echoes of the sharp clash that the israeli action provoked between the Carter administration and Prime Minister Menachem Begin's government continues to swirl around the talks yesterday.

The State Department announced that the talks "made further headway" yesterday in contacts between the United States and both the Egyptian and Israeli delegations.

Vance will meet at 10 a.m. today with Begin, who is arriving for a U.S. visit, to review the progress of the talks. Before leaving for New York, Vance will also meet here with Israeli Foreign Minister Moshe Dayan and Defense Minister Ezer Weizman as well as the Egyptian delegation.

Although President Carter will be in New York City during Begin's visit, the White House ruled out the possibility of a meeting between the two leaders.

Carter's reluctance to see Begin caused speculation about whether it was intended as a snub to express U.S. disapproval of the Israeli action about the West Bank settlements.

Similar speculation also centered on the canceling of a press conference that Carter tentatively had scheduled for yesterday. Some sources said he wanted to avoid public comment on the U.S. Israeli dispute and his reasons for not meeting with Begin.

There also were suggestions in the Israeli press yesterday that Washington was trying to put pressure on Israel by postponing the visit there of Assistant Defense Secretary David E. McGiffert. he is supposed to head a mission to discuss U.S. aid in helping Israel to defray the costs of relocating its military forces from the Sinai peninsula after a peace accord with Egyptis signed.

Pentagon and State Department spokesmen refused to give any reason for the postponement of McGiffert's trip or say when he might go. They noted, though, that a lower-level Pentagon team will leave Sunday for Israel to begin consultations on two air bases the United States has agreed to help build in the Negev after Israel evacuates the Sinai.

However, it appeared that the administration took different approaches to the two missions because they are different in nature and purpose. The team that will go to Israel Sunday will be performing a purely technical job, while McGiffert's mission has overt political overtones that are tied to successful completion of an Egyptian - Israeli peace accord and the removal of Israeli forces from the Sinai.

The administration is thought to believe that the peace talks here have not yet chalked up sufficient progress to justify sending McGiffert to Israel at this time. However, if the negotiations continue to make progress, the expectation is that the timing of his trip will be arranged to match that forward movement.

George Sherman, a State Department press officer serving as spokesman for the talks, said that at yesterday's meeting the United States introduced a "clean draft" of the treaty, setting out both the language that has been agreed upon and the areas where disagreements persist.

Sherman cautioned that this was a "purely mechanical device" to aid the negotiators. He stress that, unlike two earlier drafts prepared by the United States at different stages of the negotiations, this new document does not contain any new ideas or proposals intended to reconcile disagreements.

Under Vance's guidance, Sherman said, the negotiators were going throught the entire treaty package. He characterized the talks yesterday as "serious and systematic."

"Overall, the negotiations continue to move forward," Sherman said, "but before we can be successful we still habe to have an agreement on a treaty package."

Sherman also said he could not predict when there would be another session involving the heads of all three delegations. The chief Israeli negotiators, Dayan and Weizmen, are expected to join Begin in New York today; further high-level talks would have to wait for their return to Washington.