An acrimonious dispute over U.S. policy in Central America that saw Carter administration officials and aides to President-elect Ronald Reagan exchanging angry charges threatened yesterday to jar the previously harmonious transition from Democratic to Republican control of foreign policy.

The exchange began when two of President Carter's ambassadors -- Robert White in El Salvador and Lawrence Pezzullo in Nicaragua -- told The Washington Post in interviews this week that Reagan's supporters were undercutting their authority by encouraging rightist forces seeking to foster military dictatorships in the region.

The accusations by the two career Foreign Service officers were supported by Patt Derian, assistant secretary of state for human rights. In an interview Thursday with the Asociated Press, she asserted that comments by Reagan's foreign policy advisers had contributed to the murders of four American women missionaries in El Salvador and had put White in danger of assassination attempts by rightist extremists there.

Yesterday the Reagan team fired back. Reagan's chief aide, Edwin Meese III, angrily questioned "the professionalism" of the two ambassadors, charged them with making "reckless accusations" and asserted: "At no time has any member of the transition . . . made any statement which is either intended or in fact should undercut the positions of any ambassadors anyplace."

One of Reagan's senior foreign policy advisers, Fred Ikle, called Derian's remarks "totally irresponsible" and added that in view of the violence besetting El Salvador, it is statements such as hers that could incite threats against White.

The fallout from the dispute reached the White House, where presidential press secretary Jody Powell, while noting that the ambassadors' comments "were their own," added "But they do reflect the problems that have been created in this hemisphere by leaks of transition papers and comments of people who do not represent the incoming administration but purport to do so."

Powell and spokesmen at the State Department tried to tamp down the situation by stressing that Meese and other senior members of the Reagan team have sought to clarify matters and deplore leaks coming out of the transition apparatus.

However, some important Reagan supporters clearly were not in a mood to cool off the dispute. Sen. Jesse Helms (R-N.C.), an arch conservative who will be chairman of the Senate subcommittee on hemispheric affairs in the new Congress, issued a statement demanding White's resignation and calling him "one of the most irresponsible and inept ambassadors that the United States has ever sent abroad."

This barrage of accusations came as the State Department confirmed that a special commission sent by Carter to El Salvador to look into the Dec. 3 murder of the missionaries -- three Roman Catholic nuns and a lay social worker -- had reported that "thus far there was no direct evidence of who committed the crime." But, a department statement added, there is "circumstantial evidence" of possible involvement by Salvadoran security forces that requires further investigation.

The report went on to say that resumption of $25 million in U.S. aid to El Slvador, suspended by Carter after the killings, will depend on Salvadoran authorities conducting a thorough investigation of the murders and on whether negotiations between civilian moderates and the military lead to restructuring of the ruling junta in a way that will make it better able to control the violence and carry out reforms.

The Salvadoran situation is one of the causes of the dispute that broke out this week between the Carter and Reagan camps. The Carter administration has followed a policy of trying to work with leftist forces in Central America. That has meant support for the radical Sandinistas now controlling Nicaragua and for the civilian-military junta that seized power in El Salvador 15 months ago in an effort to reconcile that country's warring factions of the extreme right and left.

However, this U.S. policy was attacked by Reagan and his supporters during the presidential campaign as playing into the hands of forces that allegedly are controlled by communist Cuba. Last week, conservatives in the Reagan camp leaked to the press a preliminary report prepared by a member of Reagan's State Department transition team, Pedro Sanjuan, that sharply questioned the Carter policy, and an alleged ambassadorial "hit list" that marked White and Pezzullo for removal as liberal "social reformers."

That led the two envoys to hit back with charges that Reagan's advisers were encouraging Central American rightists to resist democratic change and seek to foment military dictatorship. Both accused Cleto Di Giovanni Jr., a former CIA officer with ties to Reagan supporters, of carrying that message to the region, but Reagan transition officials have denied that he has any official connection to the Reagan camp or any authority to act on its behalf.

However, a senior White House official, who declined to be identified, said the ambassadors and Derian "didn't begin this process. All three have been commented on in a rather derogatory fashion . . . . You can't expect human beings to sit there forever and not comment in their own defense."

Robert Neumann, head of the State Department transition team, said that on Nov. 24 messages had been sent to all embassies advising them to check on the authenticity of anyone who might show up purporting to represent the Reagan team, but that neither White nor Pezzullo had done so. Neumann also said ambassadors on the alleged "hit list" had been advised that it was not an official document and was creating an "erroneous impression" about the incoming administration's intentions.