The Reagan administration sent messages to President Ferdinand Marcos that time had run out for his regime through three separate private channels last Sunday evening, nearly 12 hours before this viewpoint was made public in an early morning White House announcement, U.S. and Philippine sources said yesterday.

The messages to the Philippine president flowed from a crucial National Security Council meeting Sunday afternoon at which special U.S. envoy Philip C. Habib reported bluntly to President Reagan that "the Marcos era has ended," sources said.

Philippine First Lady Imelda Marcos, opening her own line of communication to Washington, telephoned Nancy Reagan as the end neared on Monday. Mrs. Reagan urged Mrs. Marcos to avoid violence and bloodshed and expressed concern for the safety of the Marcos family, saying "if they want to come to the United States they certainly could," according to Elaine Crispen, Mrs. Reagan's press secretary.

Earlier, on Sunday evening, Secretary of State George P. Shultz and Undersecretary of State Michael H. Armacost spoke bluntly at the State Department to Blas F. Ople, Marcos' minister of labor and head of a three-man delegation sent by Marcos to Washington last week. Ople said in an interview yesterday that Shultz and Armacost told him "that the time of President Marcos had run out, that by and large he had lost control of his army, that the troops under Gen. [Fabian] Ver were inert or uncooperative, that his life was in danger and that if he did not step down the country could be headed toward civil war."

Ople, who was one of the three channels through which the message was passed to a reluctant Marcos, said he informed Marcos at the behest of U.S. officials that "the United States would facilitate the safety and medical services" for Marcos, his immediate family and close associates if the Philippine president abdicated without further bloodshed.

At the same time, U.S. sources said, the same message was being relayed through U.S. Ambassador Stephen Bosworth in Manila.

A third channel was Marcos' special adviser for commercial matters, Alejandro Melchor, who like Ople was in Washington on a mission for Marcos. Melchor, a graduate of the U.S. Naval Academy, was briefed by White House national security affairs adviser John M. Poindexter.

Interviews with several persons involved in confidential Washington discussions during the tumultuous final days of Marcos' reign indicate a timetable for U.S. decisions and actions somewhat different from the one made public in the immediate aftermath of the Philippine leader's flight from Manila Tuesday.

The crucial time in Washington decision-making now appears to have been the meeting of the National Security Planning Group, a top-level committee of the National Security Council, from 3:03 p.m. to 4:28 p.m. last Sunday.

The public result of that meeting was a U.S. statement by White House spokesman Larry Speakes at 5:15 p.m. that U.S. military aid to the Philippines would be cut off if troops loyal to Marcos used force against breakaway military elements headed by Defense Minister Juan Ponce Enrile and deputy chief of staff Fidel Ramos.

Speakes said it is "not our prerogative" to ask Marcos to step down. Officials said Speakes was trying to limit his announcements to the threatened cutoff of U.S. military aid.

The crucial Planning Group meeting began with a presentation by Poindexter, followed by an intelligence report from CIA Director William J. Casey and a military report from Defense Secretary Caspar W. Weinberger.

Habib then presented his report on his meetings with church, political and business leaders -- by his account, nearly 100 meetings in all -- during his week of fact-finding in Manila.

After Habib declared dramatically that "the Marcos era has ended," Shultz backed up the envoy with a strong presentation.

Informed sources said Shultz told Reagan that there was a consensus among his advisers that Marcos could not last long. "Not a person here" believes Marcos can remain in power, Shultz said, adding, "He's had it."

At one point White House chief of staff Donald T. Regan expressed the view that it was too early for the United States to seek Marcos' departure because of uncertainty about the identity and policies of his successor, according to two participants. Regan recalled the downfall of the shah of Iran and the rise of Ayatollah Ruhollah Khomeini as a change that made the situation worse from the standpoint of American interests.

Shultz and Habib argued forcefully that Regan was wrong.

The president indicated that he wanted to nudge rather than push Marcos, partly for fear that the Philippine president would only "dig in his heels" at a U.S. message urging him to step down. While Reagan did not explicitly approve such a message at that moment, a senior official said, he did endorse the general strategy.

A direct telephone call from Reagan to Marcos and another mission to Manila by Sen. Paul Laxalt (R-Nev.) were discussed during the meeting as ways to inform Marcos that his time was up. These were rejected in favor of discussions with the emissaries, in part because of the publicity Laxalt's mission would attract and in part because of concerns that the Soviets or others could electronically eavesdrop on a call from Reagan to Marcos. (Laxalt became another conduit for messages when Marcos telephoned him on his own initiative at 1:45 p.m. Monday to take another reading on Reagan's thoughts.)

The "talking points" for the Marcos emissaries and the instructions for Bosworth, which made it clear Marcos should surrender power, were drafted by Shultz and others shortly after the Planning Group meeting ended. A senior State Department official said these were cleared by Reagan.

After Ople met Shultz and Armacost at the State Department Sunday evening, he tried in vain to telephone Marcos in Manila. Because all lines were tied up, Ople settled for a written message to Marcos sent about 2 a.m. Washington time through the Philippine Embassy.

About 6:30 a.m. Ople received a telephone call from Marcos asking about the message.

"I told President Marcos that it seemed that President Reagan's mind was firmly made up, that there could be no appeal from it," Ople recalled. "I stressed the point that they were ready to receive him in the United States not as a villain fleeing from the wrath of the people but as an old friend and ally who could spend the rest of his days in America as an honored guest."

By this point, said Ople, "His [Marcos'] emotional calm had been shattered. He was very indignant about the manner in which the U.S. government had treated him."

Marcos resisted leaving, and he told Ople that the First Lady "is here beside me. She doesn't want to leave."

The Philippine president also protested that the breakaway forces were waging "aggression" against him. "My life and the lives of my family are threatened right here. They have bombed the palace. They have forcibly taken over the radio station," Marcos was quoted as saying.

Yet at the same time, Marcos complained, he was being told not to deploy his own military forces against his opponents. "He said it was a very curious situation, in which he is being told not to defend himself . . . by the United States," Ople recalled.

Up to the final hours, according to U.S. sources, Marcos continued to hope that he could retain some authority in a transition government in which his foes had a dominant role. It was not to be. Marcos was told, through various intermediaries, that it was too late for him to remain even as a figurehead.