"The UN Human Rights Council (HRC) should urgently establish a commission of inquiry into the situation in the central Kasai region," said a coalition of 262 Congolese and nine international NGOs, including Human Rights Watch and Amnesty International.
The central Kasai region has seen a major spike in violence since September when government forces killed a tribal chief and militia leader called Kamwina Nsapu who had rebelled against President Joseph Kabila.
The UN has also reported finding 40 mass graves, with two of its researchers investigating the violence abducted and killed.
"The violence in the Kasai region has caused immense suffering, with Congolese authorities unable or unwilling to stop the carnage or hold those responsible for the abuses to account," said Ida Sawyer, Central Africa director at Human Rights Watch.
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"An independent, international investigation is needed to document the abuses, identify those responsible, and help ensure justice for the victims."
In May, the UN Security Council expressed doubts about Kinshasa's ability to independently probe the murder of the UN experts.
Last week, the Congolese public prosecutor said he was investigating allegations that former development minister Clement Kanku may have been linked to the murders.
"We cannot expect anything from such national investigations," Rostin Manketa, who heads the Kinshasa-based rights group Voice of the Voiceless, told AFP.
Kabila himself went to Kasai on Tuesday on his first trip there since the violence erupted.
It also imposed sanctions on nine Congolese officials, including the intelligence chief and several ministers, some of whom are accused of serious rights violations in Kasai.
The UN children's fund has warned that the violence has put nearly 400,000 children at risk of dying of hunger in Kasai due to disrupted food supplies.
The unrest has also sent thousands of people fleeing to neighbouring Angola where UN figures in mid-May showed some 20,000 people were sheltering.