The Southern Command of the U.S. armed forces expects to keep a 1,200-man military task force on duty in Honduras "for the next three to five years" and is already working on detailed engineering plans for the year 1990, according to an internal Defense Department document.

A letter from an Air Force civil engineering officer at Southern Command headquarters in Panama to the Tactical Air Command at Langley Air Force Base in Virginia contradicts Reagan administration assertions that the U.S. presence in Honduras is maintained on an annual basis and is intended only to support ongoing military exercises.

Defense Department officials said the letter reflected "the author's own planning assumptions" and "does not necessarily reflect U.S. or Honduran policy."

The Southern Command, which covers Central and South America, has held regular military exercises in Honduras since 1983 involving up to 6,600 servicemen. The maneuvers are part of the U.S. effort to pressure the leftist government of neighboring Nicaragua toward democratic reforms, as are an estimated 12,000 Nicaraguan contras, who are fighting the Nicaraguan government from bases in Honduras with U.S. help.

About 1,200 U.S. servicemen in a unit called Joint Task Force Bravo remain in Honduras between exercises to help maintain the U.S.-built facilities and train Honduran troops.

The unclassified May 29 letter, the first page of which was photocopied and provided to The Washington Post, was addressed to Brig. Gen. Roy M. Goodwin, deputy chief of staff for civil engineering and troop support services at the Tactical Air Command at Langley. According to William H. Ormsbee, spokesman for the Southern Command in Panama, the letter was sent by Lt. Col. Philip Stowell, the base civil engineer.

The first page discussed an agreement with the Honduran government signed during recent negotiations on overall relations between the two nations.

"The 24th Civil Engineering Mission in Honduras has expanded" because of that pact, the letter said, and will have to develop "long range master planning for the five aerial ports," or airports, at Palmerola, Goloson, La Mesa, Toncontin and Trujillo.

All five are U.S.-built or -improved airports owned by Honduras, which has become the United States' strongest military ally in the region. "We are now working the Palmerola 1990 plan," the letter said.

The letter said that "CINCSOUTH," or Gen. John R. Galvin, commander in chief of the Southern Command, "recently reviewed all engineering activities in Honduras and provided the following guidance:

"A. JTF-Bravo at Palmerola will be in place for the next 3 to 5 years.

"B. Better facilities are needed to replace the wooden CAT [Central American Tropical] HUTS for safety, security and quality of life -- modular structures," Stowell's letter said.

Ormsbee said Stowell was on leave, but that "what he stated as CINCSOUTH guidance was verbal and really is just his [Stowell's] planning assumption, planning factors he misstated as guidance." The letter, he conceded, "could have been worded differently."

Another senior Defense Department official said, "It is not the Defense Department decision that [U.S. forces] should be in place three to five years." He added, "As seen here, it's temporary. If it's needed next year, it will be continued next year. If not, it will be stopped."

The letter continued that the engineering unit in Panama expects to develop a further agreement with Honduras "on land use, maintenance and repair of common vertical facilities [buildings], utilities and roads for the five aerial ports . . . and act as liaison for future negotiations."

The letter is the latest of several recent indications that the U.S. presence in Honduras is expanding. Richard L. Armitage, deputy assistant secretary of defense for international security affairs, notified Congress earlier this month that the Army will reprogram $140,000 for two sophisticated helicopter maintenance shelters at Palmerola.

The administration last month renewed a $3.2 million reprogramming request to build a new "contingency facility" at Palmerola that would house "operations, troop quarters, dining, recreation, administration and supply functions, an aircraft maintenance hangar and an aircraft parking apron." The House Appropriations subcommittee on military construction, which last year rejected that request, has put off the new approach for later consideration.