According to the inmates at the jail, at least two prisoners were reported killed in the melee.
People living near the prison reported the sound of several gunshots from the prison in Kinshasa.
Amigo Gonde, head of a prominent local rights group, the Association for the Defence of Human Rights, said two prisoners were killed.
"Prisoners were killed and many others were wounded by the police, who fired live rounds at prisoners who revolted against their living conditions," Gonde said.
Prison director Dido Kitunga refused to comment, but other prison officials confirmed the fatalities.
Inmates reached by mobile phones inside the prison compound said prisoners hurled stones and bottles at guards and around 10 inmates were wounded, as guards firing tear gas beat inmates back with clubs.
The inmates said the tighter restrictions included a ban on visitors, medical care and some meals.
Some 14 prisoners were discovered missing on Tuesday, though two were later captured the same day.
All were former members of President Laurent Kabila's military guard who were convicted of playing a role in his 2001 assassination.
In 2003, a Kinshasa court sentenced 26 people to death in connection with the killing, though none of the executions is known to have been carried out.
Some 64 others were sentenced to jail terms ranging from six months to life.
Current President Joseph Kabila took power after his father was killed and helped set up a transitional government with the aim of transforming the restive, sprawling Central African nation into a democratic state.
Congo is readying for a presidential runoff vote on Sunday between Joseph Kabila and Jean-Pierre Bemba, an ex-rebel leader who is now one of the country's four vice-presidents.
The runoff was required after no candidate won a simple majority in the first round in July.
UN spokesman Jean Tobie Okala called the riot an isolated incident "that will not threaten the vote."