In addition, four of the couple`s fellow parishioners were charged with assaulting the teenager`s younger brother on Sunday at the Word of Life Church in Chadwicks, New York, about 50 miles (80 km) east of Syracuse.
"Both brothers were continually subjected to physical punishment over the course of several hours in the hopes that each would confess to prior sins and ask for forgiveness," Michael Inserra, chief of the New Hartford Police, said at a news conference.
Reuters was unable to reach representatives for the accused or the church.
The older brother, Lucas Leonard, died on Monday afternoon after being driven to a hospital by family members, who falsely told doctors the teenager had suffered a gunshot wound, police said. Leonard`s injuries were consistent with blunt force trauma to his torso and extremities, police said.
New Hartford police and the New York State Police said they launched a joint investigation after being notified about the suspicious death.
Through interviews with church members, police said they learned that Leonard`s 17-year-old brother, Christopher, had also been severely beaten during the counseling session. The sessions are held after church services and are typically led by a pastor or other church member, Inserra said.
Police sent tactical teams some time between Monday afternoon and Tuesday to the three-story, red brick church, where they eventually located Christopher on the second floor.
Christopher was being treated in an area hospital for blunt force trauma to his body and extremities and was in serious condition.
Sarah Ferguson, 33, the victims` sister, and fellow church members Linda Morey, 54, David Morey, 26, and Joseph Irwin, 26, were arrested on charges of assault in the second degree. They were being held in lieu of $50,000 each.
Several children were removed from the church and turned over to Oneida County Child Protective Services.
Oneida County District Attorney Scott McNamara said there was not enough evidence to charge the couple with murder.
Additional charges and arrests were pending, police said.
Investigators disclosed little about the Word of Life Church, which describes itself on the front of its parish simply as a Christian church.
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