Sunday's massacre follows a string of attacks by radical Islamist insurgents on military posts, a mining convoy and places of worship in the restive countryside that the cash-strapped military has struggled to contain.
The assailants fled on motorbikes after spraying bullets into the Protestant congregation, authorities said.
"I offer my deepest condolences to the bereaved families and wish a speedy recovery to the wounded," Burkina Faso's president, Roch Marc KaborĂ©, tweeted late Sunday.
No group has asserted responsibility for the attack yet, but fighters linked to the Islamic State and al-Qaida routinely ambush soldiers and civilians in a campaign to sow division, gain recruits and seize territory.
Such attacks have quadrupled over the last two years in Burkina Faso, which was once known as a peaceful farming state that prized art and religious tolerance. The country of 19 million is about two-thirds Muslim, with a Christian minority.
Now the country is a hotbed for terrorism in the troubled Sahel region, which lies south of the Sahara Desert.
U.S. officials have warned that extremist groups are exploiting the remote terrain to train, forcibly recruit followers and plan attacks to carry out worldwide.
The number of deaths there is on track to increase by 60 percent this year, compared to the toll of 1,112 in 2018, according to the Africa Center for Strategic Studies in Washington.
The Burkinabe army is working with French soldiers and forces from neighboring countries to beat back the insurgency, which began after the Libyan government collapsed in 2011 and triggered a violent chain reaction in West Africa.
Armed mercenaries once hired by Libyan leader Moammar Gadhafi returned home to Mali and forged an alliance with extremists, which set off a conflict that has spilled over the border into Burkina Faso.
The church ambush in Hantoukoura follows attacks on places of worship that have killed dozens this year in the country's borderlands.
Militants summarily executed a Catholic priest in eastern Bittou in February and stormed a Protestant church service two months later in northern Silgadji, killing five.
They torched another church in the area in May and attacked a separate procession the next day, killing a total of nine. They ambushed a Sunday mass in the north two weeks later, killing four.
The gunfire is often indiscriminate, analysts say, but extremists have targeted men for wearing crosses and Muslim leaders who do not follow their rules.
Some see the church attacks as a strategy to stoke religious tensions in a country where Muslim and Christian children play together in the street.
"They are planting seeds of a religious conflict," Chrysogone Zougmore, president of the Burkinabe Movement for Human and Peoples' Rights, a victim advocacy group in the country's capital, Ouagadougou, told The Washington Post in August. "They want to create hate. They want to create differences between us."
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