“Father Sebastien was taken away by police just after morning mass,” a nun of the Saint-Robert parish told AFP in N’sele on the eastern outskirts of the capital.
A police vehicle drew up outside the church, officers jumped out and “started to beat the priest,” said another nun who had also witnessed the incident.
“They threw him in the jeep and drove off with him,” she said, adding that an unidentified man “filmed the priest” on his mobile phone during mass.
Police refused to comment on the incident when contacted by AFP.
Priest Sebastien Yebo has worked for the parish since August 2017.
The incident comes after a deadly crackdown by the government on Catholic-organised protests against President Joseph Kabila.
At least 15 people have been killed in clashes with security forces at rallies on December 31 and January 21, according to the UN peacekeeping mission MONUSCO.
Kabila, 46, has been in power since 2001, at the helm of a regime widely criticised for corruption, repression and incompetence.
His constitutional term in office expired in December 2016 but he has stayed on, stoking a bloody spiral of violence in the Democratic Republic of Congo.
Under a deal brokered by the powerful Catholic Church, he was allowed to stay in office provided new elections were held in 2017.
The authorities then postponed the election until December 23 this year, citing what they said were logistical problems in preparing for the vote.
The delay, coupled with the mounting violence, has placed Kabila on collision course with the church, which has a prominent role in the DR Congo due to its educational and social care work.