The Carter administration, despite new interruptions and setbacks, appealed again yesterday for Egypt and Israel to resume the Palestinian autonomy negotiations, the next step in the Camp David peace process.

"It is our position that the negotiations should continue," said State Department spokesman John Trattner. He described Israel's recent law declaring perpetual sovereignty over Jerusalem as "an obstacle" to the peace talks, "but not one that is insurmountable."

Administration officials involved in the effort to keep alive the Camp David process expressed frustration that such knotty questions as Jerusalem and the fate of Israeli settlements in occupied territory have become matters of controversy between the two Middle East parties.

Everyone knows and agrees that these tough problems can be resolved only at a much later stage of negotiations, the sources said, and thus it is particularly unfortunate that political controversy about them should be a barrier to immediate progress.

The U.S. argument to Egypt and Israel in the present moment is that now that each side has spoken to the other in letters and political oratory, it is time to place their long-term differences "on the back burner" for the sake of short-term progress on tangible and negotiable issues.

The argument is being made in direct communications from Washington and through U.S. diplomats in the two countries. Unless the situation changes in the meantime, this appeal is likely to be taken to Egyptian President Anwar Sadat and Israeli Prime Minister Menachem Begin in person late this month by U.S. special negotiator Sol Linowitz on a planned trip to the area.

U.S. officials conceded it is "problematical" that Sadat can be convinced to resume the autonomy negotiations at an early date. The Egyptian leader ordered a delay in the talks Aug. 2, three days after the adoption of the Jerusalem bill by the Israeli Knesset.

The strong positions taken by Begin on both the Jerusalem and settlements issues in his recent letter to Sadat did nothing to restore the talks, U.S. sources said.

On the other hand, the sources said the overall tone of the Begin letter was personal and conciliatory, and thus official Washington was less upset by the letter than might be expected on the basis of news accounts from the Mideast.

A complicating factor in the administration's drive to depoliticize the dialogue between Egypt and Israel, making it possible to move back to the details of the autonomy negotiations, is the likelihood of a United Nations Security Council special session on Jerusalem late this week or early next week. The session has been demanded by Islamic nations, with impetus from the Palestine Liberation Organization, in response to the Israeli law regarding Jerusalem.

Drafts of the proposed U.N. resolutions being circulated in New York are reported to call for the application of economic and political sanctions against Israel in retaliation for its claim to all of Jerusalem.

There is little doubt that the United States would veto a resolution containing such sanctions.Even so, the emotion and oratory generated by the debate would be likely to have polarizing effects both in Israel and the Arab world, according to U.S. officials.

Another unhealthful development in the U.S. view is the decision by European Common Market countries to undertake their own Middle East peace policy and explorations. American officials have expressed concern to the Europeans that the initiative may seem to hold out the promise of greater gains for the Palestinians that the Camp David process, even though there is no mechanism for this promise to be fulfilled.

The Carter administration, as author of the Camp David process, has little choice but to persevere in its pursuit. With all its difficulties and vulnerabilities, officials here insist, it is the only practical means available for actual Middle East peace negotiations.