Richard B. Stone, the Reagan administration's newly designated special representative to Central America, pledged yesterday to work for a negotiated settlement to the conflict in El Salvador, but said that "the odds are long" against obtaining one.

"It's a very difficult situation," Stone said, moments after his appointment was announced by White House spokesman Larry Speakes. "Anyone who thinks that a mere invitation to peace will produce peace is just inaccurate and unrealistic."

Stone, a former Democratic senator from Florida, held a short news conference in the White House briefing room that was attended at its conclusion by President Reagan, who congratulated the new special envoy and predicted that he would be confirmed by the Senate.

Reagan's prediction was echoed on Capitol Hill, but one Senate source noted that there was "a conspicuous absence" of Republican senators rushing to congratulate Reagan about the appointment.

One Republican senator said that Stone lacked the "sensitivity to diplomatic nuances" needed for the job. However, Sen. Paul E. Tsongas (D-Mass.), an opponent of the Reagan administration's Central American policies, called Stone "an acceptable nominee."

"Sure, he's going to be confirmed, because he's a former colleague," said one Senate aide. "Senators are going to hold their nose and vote for him, but they have reservations about both his competence and his views."

Sen. Charles McC. Mathias Jr. (R-Md.) disputed this view, saying that Stone would be examined carefully by the Foreign Relations Committee "and the fact that he is a former member of the Senate will not protect him from that."

The reservations about Stone in the Senate were considered so serious by the White House on Wednesday that high administration officials, after an internal dispute, agreed at the last minute to delete his announcement from the president's nationally televised speech at a joint session of Congress.

White House officials gave two reasons for the deletion. They said Stone's name was taken out because senators wanted the opportunity to be consulted before an appointment was announced and because officials wanted to hold it back and make more of an impact the following day.

Reagan alluded to the latter reason during his appearance, saying that "my own feeling was that we had enough news in the speech last night and we saved some news for today."

White House officials said that Senate Foreign Relations Committee Charles H. Percy (R-Ill.), who in the past has been critical of the administration for failing to consult with the Senate, had informed the president's advisers that the nomination was acceptable.

The conservative Stone has been criticized because he served for a year as a registered lobbyist for the rightist government in Guatemala after he left the Senate and because he is mistrusted by leftists in Central America.

There are also those who worry that naming a special envoy will escalate rather than ease the conflict in the region.

"It's wrong to have a special envoy because that puts us in a very sensitive position in the middle of things and focuses on us as a lightning rod for success or failure in El Salvador," said Sen. Nancy Landon Kassebaum (R-Kan.), on whom the administration is counting for support of its policies in the region.

Stone attempted yesterday to defuse concern about his supposed inability to deal with left-wing groups in Central America because of his identification with their opponents. Asked how he would "bring in the left if they didn't trust him," Stone replied:

"It's not a question of trusting me. It's a question of trusting the Latin nations themselves. They're going to set this agenda, and we will do our best to support that agenda."

Stone's appointment was a victory for national security affairs adviser William P. Clark, who had been instrumental in engineering his appointment to his present position as a coordinator of the administration's Central America policies on Capitol Hill.

The appointment reportedly was opposed by Thomas O. Enders, the assistant secretary of state for inter-American affairs, but Stone made a point yesterday of praising Enders "and his very capable staff" and pledged to work closely with the State Department.

There were echoes of recent White House staff conflicts in the appointment, with some Senate sources saying they had expressed reservations about Stone only after being visited by chief of legislative liaison Kenneth M. Duberstein, who told them about potential opposition to the nomination. However, there was general agreement on both sides of Pennsylvania Avenue that Reagan was accurate in predicting that Stone will be confirmed.