Former secretary of state Henry A. Kissinger said yesterday that Philip C. Habib's abrupt resignation as President Reagan's special envoy for Central America is likely to be interpreted as a sign that the administration is having "second thoughts" about seeking a negotiated settlement with Nicaragua.

"If we are not careful, we will wind up reaping only the disadvantages of every course of action," Kissinger said in a telephone interview. He spoke in reference to the confusion and mixed signals from the administration over the past two weeks as it has sought to contend with the conflicting pressures buffeting Reagan's new Central America policy.

The unexpected announcement Friday of Habib's resignation, reportedly because the White House had excluded him from a lead role in regional peace talks, underlined the divisions in the administration. The dispute centers on whether negotiations might be contrary to U.S. interests because they do not do enough to curb Cuban and Soviet influence in the region.

The Habib incident clearly was a setback for Secretary of State George P. Shultz, who is understood to have backed Habib's call for immediate, high-level U.S. involvement in any talks between Nicaragua and its neighbors. However, administration officials said that idea was overruled by the White House, which wants to avoid direct U.S. talks with Nicaragua. And it has taken a more cautious, arms-length approach to the negotiations now shaping up among the Central American countries.

Kissinger, while emphasizing that he had not spoken to Shultz, said it is obvious that "Shultz doesn't consider what happened a policy victory." Kissinger said Habib's departure will be seen by Central American governments and Congress as proof that the Reagan administration, for all its recent talk about negotiations, still considers military support of Nicaragua's contras as the best way of dealing with the leftist Sandinista government.

Kissinger stressed that he does not know the details of what caused Habib's resignation and noted that, "I speak as someone who personally favors aid to the contras." Yet, he added, the administration in the past two weeks has changed the nature of the debate over Central America through its announcement of a bipartisan U.S. peace initiative crafted by Reagan and House Speaker Jim Wright (D-Tex.). And it has offered qualified welcoming to another plan for negotiations adopted by the presidents of Nicaragua, El Salvador, Honduras, Costa Rica and Guatemala.

"What happened, starting with the Reagan-Wright initiative, was that the administration altered the terms of the debate from the wisdom of pursuing a military course with Nicaragua to a hassle over terms for cutting off aid to the contras," Kissinger said.

"The subsequent decision by the Central Americans to come up with their own variation on a peace plan was a logical extension of what the administration did," he continued. "Having taken the first step down that road, the administration cannot credibly veer away because it is uneasy about some aspects of the Central American plan and seek to alter it with changes of personnel."

Repeating an argument he has made in recent weeks, Kissinger said: "You can't carry water on both shoulders about this. It will be self-defeating. If the aim of the administration is to overthrow the Sandinistas, it should say so and get Congress to vote it up or down. If the administration is not prepared to do that, then it needs to seek formulas for an accommodation and cannot allow itself to be pressured into changing course constantly."

Habib served as assistant secretary of state for Far Eastern affairs and under secretary for political affairs -- the highest State Department post normally held by a career diplomat -- when Kissinger was secretary of state in the mid 1970s. Kissinger said yesterday:

"I don't always agree with his views, but he is one of the most distinguished diplomats of our time, and there is no doubt that he would have carried out whatever negotiating instructions he was given with total loyalty and diligence. I can't speak for Shultz, but losing Phil's services must have been very painful for him."

Administration officials, familiar with White House views, said that no one was dissatisfied with Habib and that Reagan, who has great respect for him, had planned to use him eventually in the Central American discussions. However, the officials added, the president and his principal White House advisers felt that the course advocated by Habib and, to a lesser degree by Shultz, inevitably would have meant direct talks with Nicaragua. And Reagan has decided that he does not want that at this time.

Reagan, who is vacationing at his ranch near Santa Barbara, Calif., reiterated in a radio address that he welcomes the Central American initiative and "is willing to work with our Central American friends as they perfect and implement it, consisistent with our national interests and our commitment to those fighting for freedom in Nicaragua."

"Our support for the freedom fighters should continue until a satisfactory peace plan is in place, a cease-fire has occurred and a verifiable process of democratization is under way," he added. Staff writer Lou Cannon contributed to this report from Santa Barbara.