President Reagan yesterday announced the resignation of Robert C. McFarlane as his national security affairs adviser and appointed Vice Adm. John M. Poindexter, McFarlane's low-key deputy, to the powerful foreign policy post.

Despite reports from senior White House officials of friction between McFarlane and chief of staff Donald T. Regan, the president and McFarlane denied to reporters that the resignation stemmed from such conflict.

"You have all been misinformed about that," the president said. McFarlane described reports of conflict with Regan as "nonsense."

The president and other aides acknowledged that they had assured Poindexter on Tuesday that he would have independent access to the Oval Office and would not have to report through the chief of staff.

In Poindexter, 49, Reagan opted for an adviser who colleagues say is bright, well-versed in military operations and a skilled bureaucratic operator who pays attention to details. Associates also describe Poindexter as having virtually no contact with Congress, as being "totally apolitical" and often scornful of the news media. By contrast, McFarlane had good relations with Congress, including many Democrats, and often took into account domestic political considerations in policy-making. White House officials said Poindexter, McFarlane's choice as his successor, played a major behind-the-scenes role in managing the successful interception of an Egyptian passenger jet carrying hijackers of the Achille Lauro cruise ship.

"He is a superb crisis manager, the kind of guy you'd want around if the balloon goes up," a White House aide said.

However, officials said Poindexter is untested at managing foreign policy, and five White House officials interviewed yesterday offered little evidence of his role in major policy decisions in recent years.

"I don't think he's ever had to come down on East-West issues or Central America," a senior White House official said. Another added: "I don't think anyone can tell you how he'll function."

Described as quiet and circumspect in private White House meetings, Poindexter has earned a reputation as an advocate of using military force as a tool of diplomacy.

According to a fellow admiral, Poindexter pushed hard during the Lebanon crisis of 1983 for additional U.S. military bombing and other actions in response to terrorism and to bolster the Beirut government.

While some U.S. military force was used, Poindexter was said to be frustrated that it was not stronger, and he directed that frustration at other senior policy-makers, including Defense Secretary Caspar W. Weinberger and then-Joint Chiefs of Staff chairman John W. Vessey Jr.

Associates who have worked with Poindexter say he is a bureaucratic manager. "He's a bulldog, very tenacious, a very good staff man. He knows the bureaucracy, is hard to push around," one official said. Another said Poindexter seems to fit the mold of appointees since Regan became chief of staff: low-key officials without a political base or separate agenda that could make them Regan rivals.

Poindexter's open disdain of the media is well known among White House colleagues. On the eve of the 1983 U.S. invasion of Grenada, he instructed a White House spokesman to tell a reporter it was "preposterous" that the U.S. forces were about to land there.

Praised yesterday by Reagan as a "truly steady hand at the helm," Poindexter graduated first in his class at the U.S. Naval Academy in 1958. In 1964, he earned a doctorate degree in nuclear physics at the California Institute of Technology.

One officer described Poindexter as "one of those preordained admirals" who won command of a ship in the rank of commander rather than captain and was one of Adm. Elmo M. Zumwalt's "Mod Squaders," pushed by Zumwalt when he was chief of naval operations. Poindexter is not the first military officer to run the National Security Council staff. Brent Scowcroft, under President Gerald R. Ford, and Alexander M. Haig Jr., under President Richard M. Nixon, were both Army generals. Poindexter was promoted this year to three-star vice admiral while on the White House staff. "He made admiral ashore and has never flown his flag at sea," one naval officer said. A White House official said Poindexter was not required by law to resign his commission.