PRESIDENT REAGAN paused in the middle of awarding 12 Medals of Freedom yesterday to step down from the White House East Room dais and shake the hand of one of the honorees, former senator Jacob Javits, sitting in his wheelchair and connected to a portable respirator. It was a poignant, hushed moment during the White House midday ceremony for the nation's highest civilian award.

"He was thrilled," said Javits' daughter Joy Romero. "We all were." Javits, 78, suffers from motor-neuron disease. He lost his bid for re-election in 1980.

Reagan awarded 11 other distinguished Americans the Medal of Freedom, including one posthumously to longtime University of Alabama head football coach Paul (Bear) Bryant. Bryant, who coached more winning games than any other college coach in history, died Jan. 26. Reagan called him a "true American hero."

Bryant's granddaughter, Mary Harmon Tyson, accepted the award.

In addition to Javits and Bryant, Reagan honored:

George Balanchine, choreographer and founder of the New York City Ballet; Eric Hoffer, philosopher and former longshoreman; Dumas Malone, historian and biographer of Thomas Jefferson; James Burnham, historian and founding editor of National Review magazine; James Cheek, president of Howard University; Billy Graham, evangelist; Clare Boothe Luce, author and former diplomat and member of Congress; Buckminster Fuller, educator and architect; Mabel Mercer, blues singer; and Simon Ramo, aerospace pioneer.

"These medals are in recognition of hard work and dedication . . . for America and humanity," Reagan said following an elegant luncheon of shrimp cocktail, chicken and lemon mousse. "It is called the Medal of Freedom because only in a free society such as ours can we climb as high as our dreams and energy will take us."

In presenting the awards, Reagan described the accomplishments of the honorees. He praised Balanchine's genius, saying he has "inspired millions with his stage choreography . . . and amazed a diverse population through his talents." Balanchine is ill and did not attend. Suzanne Farrell, principal dancer of the New York City Ballet, accepted the award on his behalf.

The president hailed Burnham for "shaping the thinking of world leaders" and Fuller for being "one of the greatest minds of our time."

Cheek currently is embroiled in a campus controversy for expelling the editor of Howard University's student newspaper, who had been writing negative stories about the school and its administration. As grounds for dismissal, Cheek charged that the student editor falsified her entrance exam years ago. Although she has been reinstated, pending a university hearing on the matter, her dismissal has caused student demonstrations and criticism of Cheek.

At an earlier White House briefing, deputy press secretary Larry Speakes was asked why Cheek was named. Speakes deferred to the president.

In presenting the award, Reagan commended Cheek for creating a "better life for black Americans and a better country for us all."

The Medal of Freedom has been awarded to 221 Americans since it was established by President Harry S Truman in 1945. The Truman medal first was designed as an award for "a meritorious act of service which has aided the United States in the prosecution of the war against an enemy . . ."

President John F. Kennedy expanded the award to include special service in the areas of world peace and culture. Kennedy also decided that the awards be given annually.

Now, as the highest civilian award in the nation, it may be given by the president to "persons who have made exceptionally meritorious contributions to the security or national interests of the United States, to world peace, or to cultural or other significant public or private endeavors."

Previous recipients have included ragtime composer and pianist Eubie Blake, writer Robert Penn Warren, statesman John Foster Dulles, composer Aaron Copland, labor leader George Meany, Nobel Peace Prize winner Ralph Bunche, artist Andrew Wyeth, soprano Beverly Sills and actor John Wayne.