We are assisting people who have sheltered in the hospital, the Catholic mission is helping those who are in the church, but those who are now in the mosque are completely cut off.
"The recent incidents amply demonstrate that the situation in the Central African Republic is still fragile", Guterres said.
They had succeeded in partly securing the town by dusk, said Herve Verhoosel, spokesman for the United Nations mission (MINUSCA).
Early Saturday, another Moroccan soldier died in a similar attack on the base and a nearby Muslim-dominated area.
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UN High Commissioner for Human Rights on Tuesday expressed a deep concern over escalation of violence against civilians and UN peacekeepers in Central African Republic.
During a pastoral mission in the area on May 12, Nzapalainga called armed forces to lay down their arms and met with representatives from various fronts to listen to their demands.
But according to Local Red Cross President Pastor Antoine Mbao Bogo, gunfire continued throughout the night on Sunday preventing humanitarian organizations from intervening to help the wounded and recover the dead. However credible sources have confirmed an undetermined number of civilian casualties, MINUSCA said.
The U.N.'s intervention comes as the conflict has been reaching a climax.
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A Moroccan military source said a similar attack also took place targeting a United Nations convoy earlier in the week, which resulted in injuring nine Moroccan soldiers.
Despite pledges by militias to take part in a government-led disarmament programme, militias from rival ethnic and religious groups have increased their attacks on opponents with aid workers reporting that a security void left after Ugandan and French soldiers departs had been used by the militias to their advantage.
UN Secretary-General Antonio Guterres on Sunday strongly condemned attacks against the civilian population and UN peacekeepers in the vehicle, urging authorities to investigate and bring those responsible to justice.
Auto is emerging from civil conflict, which began in 2013, with clashes between the mainly Muslim Séléka rebel coalition and anti-Balaka militia, which are mostly Christian. The country has been plagued by inter-religious violence since 2013.
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At the time, optimism inspired by the papal visit was credited with creating a climate in which a peaceful transfer of power was possible.