Ne Muanda Nsemi, a self-styled prophet and leader of the Bundu dia Kongo movement, was arrested in March after a series of deadly clashes between his supporters and police, government spokesman Lambert Mende said.
Witnesses said they had heard gunfire near Makala prison at around 4 a.m. (0300 GMT) and saw prisoners wearing blue shirts with yellow collars in the streets.
The United Nations warned its staff to avoid unessential movement around Kinshasa, saying the situation was calm but unpredictable.
Soldiers stopped young men for questioning near Nsemi’s house in the city’s district of Ngaliema and arresting some of them, a witness said.
Justice minister Alexis Thambwe told a local radio station that, aside from Nsemi, the prison’s most prominent prisoners, including political opposition leaders and soldiers convicted in the assassination of former president Laurent Kabila, had not escaped.
Nsemi has a strong following in southwestern Congo and wants to revive the Kongo kingdom, which flourished for centuries around the mouth of the Congo River.
Clashes between his followers and security forces have compounded wider tensions across Congo since President Joseph Kabila refused to step down when his mandate expired in December, raising fears of renewed civil conflict.
At least six of Nsemi’s supporters were killed earlier this year during the two-week standoff at his Kinshasa residence that led to his capture.