Encarnacion, 20, was from Santo Domingo, Dominican Republic and had been serving in the Cali mission since August 2012.
"Elder Encarnacion's passing will be deeply felt in the mission and by all who knew him," Todd said in the statement. "We grieve with his family and friends during this time of mourning and extend to them our love, prayers, and deepest sympathy."
The LDS Church was not able to immediately provide the number of missionaries who have died this year, or in past years. News reports suggest there have been at least five missionaries who have died in 2013.
Encarnacion's death came less than a week after missionary Jason Wiberg was fatally hit by a car while on bicycle in Kuching, Malaysia, on Aug. 25. Wiberg, 19, of Roy, had been on mission since October.
The Associated Press contributed to this report.
Five LDS missionaries who have died in 2013
José Daniel Encarnacion Montero • The 20-year-old from the Dominican Republic was killed Saturday in Colombia by a stray bullet.
Jason Wiberg • The Roy 19-year-old was fatally hit by a car while riding a bicycle Aug. 25 in Malaysia.
Josh Burton • The 23-year-old, of Alberta, Canada, died July 22 in Guatemala when a truck he was riding in overturned.
Siosiua "Josh" Taufa • The Salt Lake City 20-year-old was electrocuted in Guatemala while trying to fix a family's leaky roof. Taufa was the son of Utah Highway Patrol Sgt. Aiveni "Ivan" Taufa, a member of Gov. Gary Herbert's security team.
Alesa Renee Smith • The 22-year-old, of Benton, Ark., was killed in Woodward, Okla., when she was hit by a truck while on her bicycle.
The Associated Press