The ministry said Kirk Woodman's body was found 100 kilometers (62 miles) from the site where he worked for Progress Mineral Mining Company. Woodman's son, Matt Woodman, emailed The Associated Press confirming his father's death.
"Kirk was a loving and hardworking husband, father, son and brother," he said in the email. "Not a day will go by that he won't be missed. Our family would like to thank everyone for the love and support we've received, but we ask for privacy while we grieve during this difficult time."
Woodman was kidnapped Tuesday night during a raid on a mining site in Tiabongou, about 20 kilometers (12 miles) from Mansila in Yagha province. The prefect of the rural commune of Sebba in that province, Felix Ouedraogo, said the body of a white man riddled with bullets was transferred to a hospital in Dori by defense and security services.
Burkina Faso recently declared a state of emergency in the region as attacks by Islamic extremists increase. The country's foreign minister, Alpha Barry, said it was with great emotion and sorrow that the government learned of Woodman's death.
"The government of Burkina condemns with the utmost energy this cowardly assassination and reassures that an investigation is opened and all the measures will be taken to find and punish the guilty," he said in a statement posted on Facebook.
Woodman was vice-president of exploration for Progress Minerals, according to his LinkedIn page. "This is a terrible crime and Canada is absolutely committed to working with the authorities in Burkina Faso to bring those responsible to justice," said Foreign Minister Chrystia Freeland. "Our first thought is with his family and friends who received really dreadful news."
West Africa's vast Sahel region has seen a number of abductions of foreigners in recent years by extremists linked to al-Qaida or the Islamic State organization. Woodman is the second Canadian to go missing in Burkina Faso in recent weeks, according to Burkina Faso Security Minister Clement Sawadogo.
Quebec resident Edith Blais, 34, and her Italian friend Luca Tacchetto were travelling by car in the southwest when all communication with their families abruptly ended Dec. 15. Sawadogo referred to their disappearance as a kidnapping.
Burkina Faso's security situation worsened last year with an attack on the army headquarters and the French Embassy in March. The extremist threat has shifted from the northern Sahel region, home to radicalized local preacher Ibrahim Malam Dicko, into the forested east near the border with Niger.
Burkina Faso is part of a five-nation regional counterterror force, the G5 Sahel, launched in 2017.
Gillies reported from Toronto.
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