President Carter met with Egyptian Prime Minister Mustapha Khalil yesterday amid signs that the stalled Middle East talks, although likely to resume here shortly, are far from agreement on an Egyptian-Israeli peace treaty.

At the three-hour White House meeting, Khalil gave Carter a letter from President Anwar Sadat outlining Egypt's reservations about the proposed treaty draft submitted by the United States to Israel and Egypt on Nov. 11.

Carter, speaking at a news conference Thursday, said he was "somewhat discouraged" by the failure of the 7-week-old negotiations to reach an accord. After yesterday's meeting, Secretary of State Cyrus R. Vance was asked if the president still felt the same way.

He replied: "I think the president would say that the talks were useful."

Vance, who said that he and Khalil will continue the discussions today, also acknowledged that Israel is willing to send its negotiators back to the U.S.-mediated talks here. "They have said they will return at such time as it would be useful to do so," he said.

But both he and Khalil added that they do not know when the talks, suspended for almost three weeks, will resume.

Prime Minister Menachem Begin's government previously had said it would accept the Nov. 11 draft, with the exception of one key element in the treaty package. The Israelis refused to agree to a specific timetable for carrying out negotiations to establish limited Palestinian autonomy on the Israeli-occupied West Bank and in the Gaza Strip.

However, the problem of the socalled "Linkage" between an Egyptian-Israeli treaty and the West Bank negotiations is the chief reason for Egypt's reluctance to accept the Nov. 11 draft in its present form.

Sadat has come under increasingly heavy pressure from other Arab states not to do anything that could be interpreted as making a separate peace with Israel at the expense of the Palestinians. Accordingly, he wants changes in the treaty package that would protect him against such charges.

His views were contained in the letter given to Carter yesterday and in a separate letter that was relayed to Begin Wednesday by Senate Majority Leader Robert C. Byrd (D-W. Va.), who has been traveling in the Middle East.

Although Vance and Khalil refused to discuss the Egyptian demands, their basic form has been known for several days -- a fact that was confirmed yesterday by leaks from Israel about the contents of Sadat's letter to Begin.

Specifically, the Egyptians want a timetable, or at least a target date, for the establishment of Palestinian self-government in the West Bank and Gaza. They also want the elimination or watering down of an article in the treaty stating that it must take precedence over Egypt's other treaties, including those committing it to the defense of other Arab countries that might be attacked by Israel.

Khalil said yesterday, "In my opinion, the letter [from Sadat to Begin] is very important and opens the way to further negotiations."

Privately, the Egyptians have made clear they would be willing to drop their previous insistence on a West Bank-Gaza detailed timetable in exchange for Israeli agreement on a nonbinding target date for Palestinian autonomy in those areas.

The Egyptians also have signaled their willingness to give private assurences that they will respect the idea of the treaty's prohibition of further war with Israel even if it is not specifically spelled out in the text.

Israeli sources, though, have countered that the article stating the treaty's primacy over other agreements represents the core of any Israeli-Egyptian accord and must be expressed in clear language within the treaty text if the document is to have any meaning.

In a related development yesterday, Rep. Paul Findley (R-Ill.), who met recently with Palestine Liberation Organization chief Yasser Arafat, urged the Carter administration to open talks with the PLO. Findley said Arafat had promised that, in exchange for establishment of an independent Palestinian state, the PLO would make its peace with Israel and give it de facto recognition.