Security forces stepped in after hundreds gathered in the town's main street on the last day of a three-day mourning period called by civil society groups over the murder of dozens of people on Saturday night.
Police and troops fired tear gas and warning shots to break up an angry protest in the town of Beni where 51 civilians were hacked to death, in the latest in a string of attacks blamed on rebels.
The United States has warned of more violence in the Democratic Republic of Congo, should President Joseph Kabila hold on to power after his mandate expires in December.
The civilian killed Wednesday was shot by a policeman at point blank range, according to a witness who would not be named. The head of Beni's civil society movement Gilbert Kambale also said the young man was killed by a policeman.
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At least six demonstrators were arrested in a violent manner and thrown into a military jeep to be taken to an unknown destination, an AFP reporter on the scene said.
Tensions remained high by early evening, with sporadic gunfire while demonstrators continued to barricade some streets.
The deadly protests came a day after Prime Minister Augustin Matata was booed by hundreds of demonstrators outside Beni's town hall, where he gave a short speech after a three-hour whistle-stop visit.
Matata visited the massacre site along with senior army and police officials.
"What did he come for? We don't need humanitarian aid, but peace," said Germain Katembo, a survivor of the weekend massacre who lost three members of his family.
The killings have been blamed by the government and the UN mission in the country on the rebel Allied Democratic Forces (ADF), a partly Islamist armed group of Ugandan origin.