There was evidence of a struggle in Townsend's apartment in the Valley of Peace in Belize, the Edmonton Journal reported.
Guatemalan authorities found a body floating in the Mopan River Dec. 27 but it was not positively identified until days later.
Police in the Benque Viejo area of Belize said once the body was confirmed to be Townsend's the case was upgraded from a missing person to homicide investigation.
Townsend's death was reported by his family on Facebook Thursday.
"With grieving hearts we inform you that the body found in Guatemala is Brian Townsend," wrote Ian Lund, an in-law of the family. "We want you to know how much it meant to us, the support and prayers we received from all of you. We have celebrated what Brian has been able to do in Belize and the difference he has made in the community of the Valley of Peace."
Townsend, a former physical education teacher, first visited Belize in 2001 on a mission trip, said John Murley, senior pastor at Edmonton South Seventh Day Adventist Church.
Nine years ago, Townsend moved to Belize and helped start a vocational school in the Valley of Peace community.