Mali's military junta troops carried out a coup in March.
Military officials initially asserted that Malian troops opened fire after fearing the men were jihadists, but they were apparently unarmed and it was unclear what connection, if any, they had to the jihadist rebellion controlling the massive, arid north of the West African nation.
In a statement late on Sunday, the government said "an incident" occurred overnight on Saturday in which eight Malians and eight people from neighbouring Mauritania were fatally shot.
"On behalf of the people of Mali, the government deeply regrets this painful event and presents its sincere condolences to the bereaved families and the government and people of Mauritania," the statement said.
Mauritania's official news agency AMI said 12 Mauritanians had been killed.
The Mali statement did not provide additional information but various officials said the shooting unfolded as a vehicle carrying a group of people approached a checkpoint in Diabali, a remote agricultural town in central Mali, about 400km north-east of the capital Bamako.
The army opened fire on a vehicle after the driver failed to obey commands to stop, local military sources, police and security ministry officials said. No troops were injured.
'Enemies'
Soldiers were forced to shoot because they presumed the travellers were militants, officials said.
"Sixteen members of the Dawa sect who would not stop their vehicle after warning shots were fired were treated as enemies in Diabali Saturday night," a security ministry official said.
Dawa, which one Malian official said has roots in Pakistan, has several hundred followers in north Mali and is present across the Sahel region including in neighbouring Mauritania. Iyad Ag Ghaly, who heads the Ansar Dine group, is supposed to have been a member.
But Dedi Ould Mohamed Mokhtar Ould BouEly, speaking to Agence France-Presse from the Mauritanian capital Nouakchott, said the men were 16 young preachers heading to a meeting in Bamako.
His cousin, Oumane Ould Eleyat, was among the dead.
"They were killed in cold blood by the Malian army, which is looking for any reason to ignore and hide the facts," Ould BouEly said. He claimed 10 of the dead were from Mauritania.
'Religious meeting'
According to several Malian and Mauritanian officials, the victims were travelling in a single vehicle and were unarmed.
Malian troops are on high alert after militants seized control of more than half of the country following a disastrous army coup in March in Bamako that led to political chaos and a collapsed military presence in the north.
A Diabali resident said earlier those killed had been on their way to a "religious meeting", but did not give details.
The shooting came after rebels captured on September 1 the city of Douentza, located along a rough east-west line bifurcating the country, marking the southernmost town seized by militants.
A hotchpotch of militant groups now controls the north, an area bigger than France or Texas, and in areas under their control they have enforced strict Islamic law, whipping or stoning to death transgressors and destroying ancient World Heritage sites they consider "idolatrous". – AFP