A message on his official website said McKenzie had been ill with Guillain-Barre Syndrome, a disease affecting the nervous system, and died at home on Saturday.
"San Francisco," written by the late John Phillips of California band The Mamas and The Papas, became a worldwide hit in 1967 and is credited with bringing thousands of young people to the city in search of flower power and free love.
McKenzie said on the website that the song "was not so much about the city itself, but about an idea. It was more about the Monterey Pop Festival."
The singer followed tens of thousands of young people by dropping out of mainstream society in the late 1960s and moving to Virginia for 10 years following his hit song.
In the 1980s and 1990s he joined The Mamas and the Papas and toured with them until the group disbanded.
"Scott was in and out of hospital since 2010 after falling ill with Guillain-Barre Syndrome, a disease affecting the nervous system," his website said. "It is thought he may have had a heart attack in early August 2012. Staff did not want him to leave the hospital, but he wanted to be at home and passed away on 18th August 2012."
(Reporting by Jill Serjeant; Editing by Bob Tourtellotte and Leslie Adler)
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