Security forces were deployed on Monday morning and heavy gunfire was heard in the streets
The Ninjas were a major anti-government force in the 1997-99 civil war.
The violence comes weeks after Denis Sassou Nguesso won a third presidential term in a poll that the opposition said was marred by "massive fraud".
At least one police station and a government building were attacked in the Makelekele district.
The Ninjas were loyal to former Prime Minister Bernard Kolelas, the father of Guy-Brice Parfait Kolelas, who stood in the presidential election in March and got 15% of the vote.
Mr Sassou Nguesso, in power for more than 30 years, won the election with 60% of the vote.
Reuters news agency reports that on Monday morning young opposition supporters were chanting "Sassou, leave!" in Makelekele , which is in the south of the capital city.
The Congolese government has blamed attacks on government buildings in the capital, Brazzaville, on the Ninja militia group.