Five others were murdered when militants opened fire on a local church congregation in the northern town of Dablo as they gathered for mass.
"They were about 40 on motorcycles", a witness said.
"Armed individuals burst into the Catholic church..."
An attack on a Protestant church about two weeks ago left six people dead. "Shops and stores are closed", he told AFP.
The operation was ordered to free French hostages Patrick Picque and Laurent Lassimouillas who disappeared while on holiday in the remote Pendjari National Park in Benin on May 1.
Just days ago, four hostages, including an American, a Korean, and two tourists from France, were rescued in a harrowing mission that cost two French soldiers their lives.More news: Legendary actress and singer Doris Day dead at 97
More news: Felicity Huffman to plead guilty in college admissions scam
More news: UK: Nigel Farage's Brexit Party leads European Union election poll
Intelligence agencies tracked their captors across the semi-desert terrain of eastern Burkina Faso, where it appeared they would soon cross the border into Mali.
But violence has only worsened since. Over 350 people have been killed in the raids which have been attributed to a number of jihadist groups, including the Islamic State in the Greater Sahara and the Ansarul Islam group.
The attacks took place in Dablo located in the Sanmatenga Province in the country's center.
The raids began in 2015 in the north before targeting the capital Ouagadougou and other regions, notably in the east.
Germany will give an additional €20 million to Burkina Faso and over €35 million to Niger ($22.4 million and $39 million, respectively) to support development projects as well as the outfitting and training of police officers in each country, she said.
Roughly 55 per cent to 60 per cent of Burkina Faso's population is Muslim, with up to a quarter Christian.