The west African nation's main Tuareg-led rebel alliance, the Coordination of Movements of Azawad (CMA), said in a statement overnight that "the Malian army conducted the summary and public executions of nine people in the town of Tin Hama" on Thursday.
"The nine people were first arrested by the GATIA militia and then handed over to Malian soldiers who then executed them," the statement said, referring to the pro-government Imghad and Allies Tuareg Self-Defence Group.
The information could not be independently verified, and no one from the Malian army was available for comment.
But the government rejected the allegations, saying the killings were part of a "bloody settling of scores between armed groups belonging to the locality" in a statement which accused the CMA of killing three civilians.
The government said CMA rebels attacked Tin Hama on Wednesday and were pushed back by Malian troops who seized "important war materials".
It said it was "surprised" by allegations of abuses committed by the army, adding that the administration "strongly condemns these unfortunate acts against innocent people".
It did not confirm the reports but said executions of civilians "would constitute grave crimes for which the perpetrators must be brought to justice".
Tin Hama is situated near the flashpoint town of Menaka, seized from rebels by pro-government fighters on April 27 in an operation which has sparked numerous violations of a ceasefire agreement in the area.
The UN peacekeepers expressed "deep concern at the alarming escalation in armed confrontations in several localities of northern Mali and once again condemns the gross and continuing violations of the ceasefire that jeopardise the peace process".
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