President Reagan said yesterday that he apologized to Iran on Sunday for the USS Vincennes' shooting down of an Iranian passenger jet over the Persian Gulf that killed all 290 persons aboard and declared that reparations or compensation to the families of victims are "a matter that has to be discussed."

Reagan, a White House spokesman disclosed yesterday, sent a five-paragraph diplomatic note expressing "deep regret" to the Iranian government on Sunday, shortly after U.S. military leaders learned that the guided-missile cruiser had destroyed the Iran Air A300 Airbus after mistaking it for an Iranian F14 fighter plane.

The president's message sought to assure the Iranian government that the attack was an accident, White House spokesman Marlin Fitzwater said.

Reagan, speaking to reporters as he boarded a helicopter for a visit to ailing Salvadoran President Jose Napoleon Duarte at Walter Reed Army Medical Center yesterday afternoon, replied "Yes" when asked if he considered his message to Tehran an apology.

Amid these conciliatory gestures by a leader who has repeatedly denounced Iran, Defense Department officials yesterday revealed new details of the incident that in turn raise new questions about the circumstances of the disaster.

Pentagon officials said they had learned that the Airbus may have been flying higher than originally believed and that the military aircraft signal the Vincennes reported receiving may have come from a separate plane. In addition, House Armed Services Committee Chairman Les Aspin (D-Wis.) said Defense Department officials said for the first time at a Capitol Hill briefing yesterday that the Airbus was in its assigned commercial air corridor.

At a briefing, a Pentagon spokesman said electronic data from another U.S. warship in the Persian Gulf, the frigate USS Sides, indicates that the Airbus may have been at an altitude of 12,600 feet when it was hit by a U.S. surface-to-air missile. The Vincennes reported that the Airbus was at 9,000 feet when it fired the missile. The spokesman said officials are uncertain which is correct.

The spokesman also said that classified data indicated that the Vincennes picked up two different electronic signals from the Airbus, one of which indicated it could have been a civilian aircraft, and a second, separate signal that indicated it was an Iranian F14 warplane.

Defense Department officials said they have no explanation for why a civilian aircraft would transmit electronic messages usually restricted to military planes.

"The signals . . . that the Vincennes was receiving from that aircraft were signals that we had previously identified or associated with an F14," Pentagon spokesman Dan Howard said.

However, Howard said that the frigate USS Sides, which was in the area, did not detect the same F14-like identification signals.

The Vincennes, equipped with the sophisticated Aegis electronic combat system, shot down the aircraft as it approached within nine miles of the ship, just minutes after the cruiser had exchanged gunfire with three small Iranian boats.

Defense Department officials yesterday disclosed new details of the "electronic information" that helped convince Capt. Will Rogers III that his ship was in danger. Joint Chiefs of Staff Chairman William J. Crowe Jr. on Sunday refused to provide details of the electronic signals, saying the information was classified.

With conflicting details raising even more questions about the incident, Pentagon officials yesterday described the previously classified electronic information picked up by the Vincennes' Identification Friend or Foe (IFF) radar system.

When the Vincennes IFF system electronically questioned the approaching aircraft, the plane responded with electronic identification codes on two separate channels, according to Defense Department officials.

One channel, called Mode 3 and used by all military and civilian aircraft, provided the Vincennes with a four-digit number used by a civilian air traffic controller to locate aircraft. Pentagon officials said that emission indicates the plane could have been a commercial jet, but said the skipper of the Vincennes would not necessarily be able to positively identify the aircraft by that number.

Even more critical, according to Defense Department officials, was a second transmission received by the Vincennes from a Mode 2 frequency used only by military aircraft. That emission indicated the aircraft was an Iranian F14 fighter plane, based on codes U.S. military officials in the region had previously identified as those used by the Iranians, officials said.

Pentagon officials declined to speculate yesterday as to why a civilian aircraft would have the two transponders. One official familiar with the systems said he has never known of a civilian aircraft transmitting on both the Mode 2 and Mode 3 channels.

Defense Department officials briefing House leaders yesterday said the military signals could possibly have been emitted from other aircraft flying in the area and been distorted by the gulf's hot, humid atmosphere, or they could have come from a plane following closely behind the Airbus, according to House members. Those theories, however, are considered only hypothetical by the Pentagon officials conducting the briefing, lawmakers said.

Officials also said the military code must be set manually on the ground before a plane takes off. One possible explanation of the dual frequencies is that Iran, in the past, has used some commercial aircraft to ferry military troops and could have outfitted the aircraft with both transponders.

The frigate Sides, operating near the Vincennes, picked up only transmissions from the airbus' Mode 3 channel, however, and had no indication of transmissions on the military frequency, Howard said.

On Sunday, Adm. Crowe told reporters that the Vincennes had received no IFF indications that the airplane was a commercial jet and refused to elaborate on what he called "electronic information" indicating the aircraft was a fighter jet. He said such information is classified.

Howard said yesterday that this was the first time the Defense Department had revealed that it knew the codes used by the Iranian military Mode 2 transponders.

Howard said the electronic signals would be only one piece of information used by the Vincennes skipper to determine whether the approaching aircraft was hostile.

But new conflicting details also have emerged involving the other evidence used by the skipper, including the location and altitude of the aircraft.

Pentagon officials told House leaders in a briefing yesterday that the Iranian aircraft was not outside the commercial aircraft corridor as originally reported by Crowe on Sunday, according to Rep. Aspin.

Aspin said he was told the aircraft was flying about four miles west of the center line of a commercial flight corridor that is approximately 11 miles wide. Crowe on Sunday said the Iranian plane was about 4 1/2 miles outside the established commercial flight corridor.

According to Aspin's briefing, the aircraft turned easterly toward the center line of the corridor to readjust its course, which sent it flying head-on in the direction of the Vincennes.

Pentagon officials said they had no immediate response to Aspin's report last night.

Defense Department officials also said yesterday that while the Vincennes reported the aircraft was descending and at an altitude of about 9,000 feet when the two Standard missiles were fired, the Sides had no indications that the plane was descending and reported it above 12,000 feet.

The air control tower at Bandar Abbas reported that the pilot had just received authorization to climb from 7,000 to 14,000 feet when the aircraft was shot down, according to the last recorded radio conversation between the plane and Iranian air controllers.

A six-person team headed by the U.S. Central Command's Rear Adm. William Fogarty arrived on the Vincennes today to begin an investigation of the incident and the conflicting information, officials said. The investigation is expected to take two to three weeks to complete, officials said.

"The investigation is a Monday morning quarterback excercise," Howard said. "But it is one in which they try to look at that period of time in which the commander of the ship had available to him to make a decision."

Howard reiterated the Pentagon's full support of the actions of the Vincennes skipper.

"The commander had a very few minutes in which to make a very crucial decision that was certainly life-or-death for {him} and for his ship and for his crew," Howard said. "And he had to make that decision based upon the information available to him at the time."

Staff writers David B. Ottaway and Chris Adams contributed to this report.