Martin Kobler, the new head of the UN's DR Congo taskforce (MONUSCO), said he would not allow "any attack on civilians," and added that "populated areas and areas where UN troops were stationed were targeted and fired at indiscriminately."
A local official who chose not to be named confirmed that three people were left "seriously injured by a bomb," as clashes between M23 rebels and government forces continued around the city in eastern Democratic Republic of Congo.
Kobler added he had ordered MONUSCO to respond, and to "take necessary measures to protect civilians and prevent the advance of the M23."
The latest bout of fighting in DR Congo, which erupted in mid-July and has flared up periodically ever since, ended an almost two-month truce between M23 rebels and government forces reached in May when UN chief Ban Ki-moon visited the region.
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The M23 is made up of Congolese Tutsi who were integrated into the army following a 2000 peace accord. They mutinied in April 2012 saying the accord was never fully respected.
The territory, near the villages of Mutaho and Kibati, has been in government hands since mid-July, he said, speaking on condition of anonymity.
M23 intelligence officer Modeste Bahati confirmed the renewed fighting but blamed the army for starting it by attacking rebel positions around Kibati.
"Our forces are holding their positions," he told AFP.
M23 occupied Goma for 10 days in November before withdrawing under international pressure and in return for a dialogue with Kinshasa.