60-year-old Major Geoff Friend was attacked on Saturday and was hospitalised, he later died.
His family have since traveled to the country and have released a statement saying their husband, father, son, brother and grandfather will be missed.
The Salvation Army published a statement on its website saying: "Geoff has dedicated his life to his ministry of faith and service and this has impacted many people in many walks of life."
It says it is "deeply saddened."
The Salvation Army said that Malawi was one of many source countries where people were found to be trafficked into forced labour or sexual expolitation and earlier in the month Major Geoff Friend traveled there to speak at a number of events.
"The Salvation Army expresses our heartfelt and sincere condolences to Lyn, Ashley, Nathan, Steven and Samuel as well as Geoff's parents, Allan and Mabel, for their considerable loss," it said.
"Geoff personified the character of The Salvation Army, being about 'Others'."
During thier 34 years with the Salvation Army Geoff and his wife Lyn had served in ministry in Victoria, Tasmania, South Australia and Western Australia.