Neshoba County Sheriff Larry Myers told The Associated Press that Killen was arrested at home without incident.
The arrest followed a day-long grand jury meeting Thursday that apparently included testimony from people believed to have knowledge about the killings.
"We've got several more to arrest, but we went ahead and got him because he was high profile and we knew where he was," said Myers.
That statement was originally thought to mean that more arrests are imminent in the 1964 civil rights case. However, it was learned Friday that Myers was talking about more arrests relating to Neshoba Grand grand jury action in general, rather than this specific case.
Myers said Killen was being held on three counts of murder. Calls to Killen's home Thursday were answered by a recording.
Neshoba County District Attorney Mark Duncan had said arraignments were planned for Friday morning.
Duncan declined to say whether the arraignments stemmed from the slayings in Neshoba County of civil rights workers James Chaney, Andrew Goodman and Michael Schwerner, but it appeared likely.
Seven Klansmen were convicted of federal conspiracy charges in the killings and sentenced to prison terms ranging from three years to 10 years. None served more than six years, but the state never brought murder charges.
The three were going to Mount Zion United Methodist Church just outside Philadelphia to investigate a fire the night they were killed.
They were stopped by Neshoba County deputies but released. They were stopped again by the Klan. The three were beaten and shot to death; their bodies were found later in an earthen dam.
The crimes were dramatized in the 1988 movie "Mississippi Burning."