The State Department official in charge of Latin American policy has proposed a "two-track" strategy in El Salvador in which the United States would promote negotiations with leftist guerrillas there while continuing to support the Salvadoran government's military efforts to suppress the rebels, administration officials said yesterday.

The proposal, by Thomas O. Enders, assistant secretary of state for inter-American affairs, touched off a lively policy battle within the administration that may require resolution by the National Security Council and ultimately by President Reagan.

Contained in a working paper yet to be formally submitted to the NSC, the Enders idea received what one official described as a "less than enthusiastic response" from national security affairs adviser William P. Clark and U.N. Ambassador Jeane J. Kirkpatrick, who is currently on a Central American trip--one purpose of which is to reassure pro-U.S. governments in the region.

Kirkpatrick is known to be skeptical of Enders' plan, which calls for negotiations through a third country, probably Spain, aimed at resolving the protracted conflict in El Salvador.

The administration until now has refused to endorse the idea that the guerrillas should, though negotiation, be given a share of power in El Salvador and has called instead for them to lay down their arms and seek to win their goals through democratic political means.

But administration sources said that Enders is concerned that Congress will insist on talks to end the civil war if the administration does not encourage them. Sen. Nancy Landon Kassebaum (R-Kan.), who served as one of the U.S. observers at El Salvador's elections last year, called for efforts to negotiate with the guerrillas.

Enders refused to discuss the issue and referred questions to a spokesman who declined to comment on whether the assistant secretary had prepared any proposal for a two-track approach. However, the spokesman added:

"Enders, when asked whether his testimony last week before the Senate and House with regard to negotiations in El Salvador represented U.S. government policy, said yes and and added that it would continue to remain so."

The spokesman then cited portions of Enders' statement last Friday to the House inter-American affairs subcommittee. In it, he said:

"Others say force the government [of El Salvador] to negotiate with its adversaries, and the killing will stop. But it won't. No Latin American government has ever agreed to negotiate as an equal with its armed opposition and survived . . . .

"If power sharing without reference to democratic principles is no solution, what is? The answer is inescapable: the cooperative development of political processes that are democratic and that provide the security as well as the means for reconciliation."

Nonetheless, administration officials said that the working paper explored the idea of making an approach to the rebels through a third country that would have standing both with the Salvadoran government and the guerrillas.

A Latin American diplomatic source said his government had been informed that Enders discussed the possibility of approaching the guerrillas in an unspecified way during talks in Madrid this week with Spanish Prime Minister Felipe Gonzalez, a leading Socialist who has long advocated a negotiated settlement in El Salvador.

Other countries reportedly mentioned by Enders as possible intermediaries include Mexico, Venezuela and Colombia.

But Spain is considered the most likely choice because its Socialist government is more acceptable to the Reagan administration than other Socialist governments and because Spain also has relatively high prestige in Latin America. Gonzalez is the leading spokesman on Latin American affairs within the Socialist International.

Administration officials stressed, however, that the Enders proposal, which one described as simply "a staff paper with no official standing," had yet to be considered by Reagan, who usually shares Kirkpatrick's and Clark's skepticism about the utility of negotiating with leftist rebels.

One official said that a showdown on the conflicting approaches could come next week at an NSC meeting, though no debate of the matter has been formally scheduled.

State Department sources, while refusing comment on whether a new approach was being weighed, stressed that Enders would do nothing in the Central America policy area that had not been thoroughly coordinated and discussed with Secretary of State George P. Shultz.

All of the principals in the policy debate except Enders, who arrived in Washington from Madrid yesterday, are currently abroad. Shultz, who has been on a Far Eastern tour, is due back tonight. Clark left yesterday for an official trip to Vienna and Munich and will not return until Sunday. Kirkpatrick is scheduled back on the weekend.

Since Shultz took over as secretary of state last summer, he has toned down noticeably the sometimes belligerent anti-Communist rhetoric used by his predecessor, Alexander M. Haig Jr., in discussing Central America. However, Shultz up to now has not changed the basic substance of policy in the region.

And there also is no indication that Reagan is receptive to a basic change at this time. He has, in private discusssions, reaffirmed his support for Kirkpatrick's views, which have emphasized a distinction between dealings with right-wing "authoritarian" groups and "totalitarians," as she would classify Communists.

Reagan was first attracted to Kirkpatrick during the presidential campaign by an article of hers elaborating this thesis, later expanded into a book, titled "Dictatorships and Double Standards."

Reagan has supported Kirkpatrick in past intra-administration disputes, notably with Haig, and he also relies heavily on the advice of Clark, who was his chief of staff when he was governor of California.

Shultz, while treating Kirkpatrick with courtesy, is understood to disagree with many of her views and some sources close to the U.N. ambassador have complained that the secretary has excluded her from important decisions.