Fraiser Glenn Cross Jr., of Aurora, Mo., was taken into custody in the parking lot of an elementary school near the scene of the shootings, and was booked on a charge of first degree murder, according to the Johnson County, Kansas, Sheriff's Office.
Cross is an alias for Frasier Glenn Miller, the former KKK leader, according to the Southern Poverty Law Center.
In a statement released Sunday night, the SPLC said it was able to identify Cross as Miller after a phone conversation with Miller's wife, Marge, in which she told them police had come to her home and told her that her husband had been arrested in the shootings.
The address listed by the sheriff's office for Cross is the same address Frazier Glenn Miller used when filing candidate papers to run for Congress in Missouri in 2006 and when he sued the secretary of state for refusing to let him on the ballot.
Among the three people killed in the shootings were a 14-year-old Eagle Scout and his grandfather, according to the family of the two.
"It is with deep sadness that we confirm the tragic loss of Dr. William Lewis Corporon and Reat Griffin Underwood (Losen) who died as a result of the injuries they sustained in today's shooting at the Jewish Community Center. Dr. Corporon was Reat's Grandfather, whom he loved very much," said a statement signed "Will Corporon, Son and Uncle."
The two were shot at the town's Jewish Community Center, Overland Park Police Chief John Douglass said. One died at the scene and the other died after being taken to a hospital, he said.
The third victim was a woman who was shot at Village Shalom retirement community, Douglass said. She died on the scene.
It was believed the shooter fired at two other people, but neither was hit, the police chief said.
"We have no indication that he knew the victims," Douglass said.
"We're investigating it as a hate crime, we're investigating it as a criminal act, we haven't ruled out anything," Overland Park Police Chief John Douglass said.
"There was a shotgun that was involved," he said. "We are exploring the possibility that a handgun was involved in the shooting at the two persons that he missed, and we are looking at the possibility of an assault rifle."
According to the family statement, Underwood was a freshman at Blue Valley High School, and participated in debate, theatre "and had a beautiful voice. Reat had a passion for life, and touched so many people in his young age." He was an Eagle Scout and "loved spending time camping and hunting with his Grandfather, Father, and brother," the statement said.
Corporon practiced family medicine in Marlow and Duncan, Okla., from 1976 through 2003, before moving with his wife to the Kansas City area to be closer to their grandchildren, the statement said.
Police had still not released the identities of the victims late this evening, but Rev. Adam Hamilton of the United Methodist Church of the Resurrection in Leawood said the two male victims were members of the church.
Hamilton led prayers for the victims' family this afternoon during Palm Sunday services.
The Jewish Community Center confirmed the shooting on its Facebook page and said it occurred near the Lewis and Shirley White Theater entrance and that the building was put on lockdown. According to the center's website, a production of "To Kill a Mockingbird" was scheduled to start at 2 p.m.
The center released a statement explaining that the shooting occurred in the parking lot.
"Our hearts go out to the families who have suffered loss on this tragic day," read the statement in part. "Our heartfelt gratitude as well to all those in Kansas City and around the world who have expressed sympathy, concern and support."
With the play scheduled to start, and being the eve of Passover, which starts Monday, the community center was busy when the shooting broke out.
Edward Dannewitz, who said his child was in the center when the attack happened, was shocked to hear what happened.
"We dropped our daughter off for dance practice and took our other daughter to Chuck E Cheese. The next thing you know, we're seeing updates on the phone saying that there's a shooting at the JCC," he said. "I figured this was one of the safest places I could drop my kid off at, and apparently it's not."
Rabbi Arthur Nemitoff, senior rabbi at The Temple, Congregation B'nai Jehudah, located about a mile from the Jewish Community Center told ABC News that police arrived after the shooting around 1:45 p.m. and have stationed a police car there as a precautionary measure.
Kansas Rep. Kevin Yoder said he was "heartbroken" over the shootings.
"Brooke and I send our prayers and thoughts to the families and victims of this tragedy and our office stands ready to provide any needed assistance," Yoder said in a statement.
As a matter of protocol the Los Angeles Police Department has stepped up patrols around Jewish-oriented locations. The New York Police Department said it was already in a heightened state of alert due to Passover holiday.