A group linked to Islamic extremists was suspected of being responsible for a bomb that went off in the Pentecostal church in the North Kivu province town of Kasindi, military spokesman Anthony Mwalushayi told the Associated Press by phone.
A Kenyan citizen found at the scene was detained, Mwalushayi said.
DR Congo's government urged people to avoid crowds and be vigilant as it conducted an investigation, the minister of communication tweeted.
Videos and photos of the attack seen by the AP showed dead bodies lying on the ground outside the church, including what appeared to be a dead child.
The injured were being carried out of the church surrounded by other people screaming.
Survivors and witnesses said the blast severed some people's limbs from their bodies.
Masika Makasi, 25, was sitting under a tent outside the church when she heard a noise that sounded like a tyre going flat, she told the AP from her home in Kasindi.
Her leg was injured in the attack and her sister-in-law, who was several metres away, died instantly, Makasi said.
"I am traumatised from seeing people die around me," she said.
Violence has wracked eastern DR Congo for decades as more than 120 armed groups and self-defence militias fight for land and power.
Nearly six million people are internally displaced and hundreds of thousands are facing extreme food insecurity, according to the United Nations.
Fighters with the Allied Democratic Forces, a rebel organisation which is believed to have links to the the Islamic State group, have carried out several attacks in Kasindi which is located on the border with Uganda.
Troops from Uganda's army have deployed to eastern DR Congo to try to stem the violence but the attacks have increased and spread.
ADF attacks since April have killed at least 370 civilians and involved the abduction of several hundred more, a report by the UN last month said.
The rebel group has extended its area of operations to Goma and into neighbouring Ituri province.
The complex militia problem in DR Congo has long produced ethnically motivated attacks and fluid alliances between multiple militias with diverse interests, Economist Intelligence Unit analyst Trupti Agrawal said.
"The church attack will work to further the narrative of (the) eastern (DR Congo) conflict taking a religious turn," Agrawal said.
"It is likely to deepen anti-Islam sentiment in the Christian majority country, particularly in the eastern provinces where Islamist rebels are most active."
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