The arrival of UN Under-Secretary General for Peace Operations Jean-Pierre Lacroix in Beni came several days after an angry mob stormed a UN base in the town in protest over a perceived failure of peacekeepers to stop militia violence.
Lacroix will visit the base of the UN mission, known by its French acronym MONUSCO, mobbed by protesters on Monday, and hold talks with the Congolese army and local authorities, a UN spokesman said.
At least seven people have been killed in clashes during the anti-UN protests this week.
The east of the Democratic Republic of Congo has been troubled for years by militia violence, but most recent attacks are blamed on the Allied Democratic Forces or ADF, a shadowy armed group with links to Ugandan Islamists.
DR Congo forces launched operations against the ADF in the restive eastern region at the end of October. But in response the ADF has carried out massacres, in an apparent bid to discourage civilians from helping the military.
Another 27 people were hacked to death on Wednesday, bringing the number of people killed in militia violence to 107 since November 5 in and around Beni.
The European Union has also condemned the "cowardly attacks" by armed groups and called for perpetrators to be bought to justice.
"Closer cooperation is needed between the FARDC (Congolese armed forces) and MONUSCO to reinforce protective measures for civilians," the European Union spokesman said in a statement on Friday.
MONUSCO, one of the biggest UN peacekeeping operations in the world, today comprises more than 16,500 military personnel and observers, 1,300 police and at least 4,000 civilians.
But it has struggled to make progress in a vast country beset by armed groups as well as an Ebola epidemic, poverty and poor governance.
Responding to criticism of inaction, MONUSCO says its troops are unable to deploy in combat without the approval of the host country and in coordination with national forces.
The DR Congo presidency earlier this week announced joint military operations with the UN to reestablish security in the Beni area.