The attackers then burned the church, looted a pharmacy and some others stores, and left in vehicles, they told Reuters.
The attack happened at about 9 a.m.as worshippers were gathering for Sunday Mass at a Catholic Church in the village of Dablo, about 90 kilometers (56 miles) from Kaya in the country's north, close to the volatile border with Mali.
Militant Islamic groups linked to ISIS and al-Qaeda have been waging an increasingly violent war against followers of Jesus in the West African nation - this is the third attack on a church over the past five weeks. "It's practically a ghost town".
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In February, a Spanish priest, Father Cesar Fernandez, was killed in a raid attributed to jihadists in Nohao in the centre of the country. Attacks have included the kidnapping of foreigners.
One of the French hostages, Laurent Lassimouillas said: "All our thoughts go out to the families of the soldiers and to the soldiers".
The other two hostages from the US and South Korean have not been named.
Roughly 55 per cent to 60 per cent of Burkina Faso's population is Muslim, with up to a quarter Christian.
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Merkel pledged millions in financial support for the restive Sahel region shortly after meeting with Burkina Faso's President Roch Marc Christian Kabore in the capital, Ouagadougou.
Last month, attackers targeted a Protestant church in the town of Silgadji, killing at least six people.
The attacks took place in Dablo located in the Sanmatenga Province in the country's center.
Around 4.3 million people have been driven from their homes in the worsening violence that has engulfed the entire Sahel region, including one million over the past year, according to United Nations humanitarian officials.
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