The six-year spying program, dubbed "Minaret," had been exposed in the 1970s but the targets of the surveillance had been kept secret until now.
The documents showed the NSA tracked King and his colleague Whitney Young, boxing star Ali, journalists from the New York Times and the Washington Post, and two members of Congress, Senator Frank Church of Idaho and Senator Howard Baker of Tennessee.
The declassified NSA historical account of the episode called the spying "disreputable if not outright illegal."
The documents were published after the government panel overseeing classification ruled in favor of researchers at George Washington University who had long sought the release of the secret papers.
The intensity of anti-war dissent at home led President Lyndon Johnson to ask US intelligence agencies in 1967 to find out if some protests were fueled by foreign powers.
The NSA worked with other spy agencies to draw up "watch lists" of anti-war critics to tap their overseas phone calls.
The program continued after Richard Nixon entered the White House in 1969, and historians say it reflected a climate of paranoia pervading his presidency.
US Attorney General Elliot Richardson shut down the NSA program in 1973, just as the Nixon administration was engulfed in scandal.
The 1975 disclosure of the NSA program, along with other domestic spying on Americans, caused public outrage and one of the senators who had been tapped, Church, led reforms that created stricter limits on surveillance and spy agencies.
But the NSA has been accused of overstepping its authority and flouting civil rights protections since the attacks of September 11, 2001.
The agency carried out warrantless wiretapping between 2001-2004 and recent revelations from US intelligence leaker Edward Snowden have exposed far-reaching electronic surveillance of phone records and Internet traffic.
The researchers who published the documents Wednesday said the spying abuses during the Vietnam War era far surpass the excesses of the current program.\
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