Daouda Maiga, governor of Menaka region, said on Saturday that motorbike-riding gunmen staged the attacks in the remote northeastern villages of Awakassa on Friday and in Anderanboucane, a day earlier.
He said Fulani members of Islamic State Greater Sahara likely attacked in retaliation for military actions supported by Tuareg in the region bordering Niger, The Associated Press news agency reported.
In recent months, Tuareg civilian defence groups, supported by French soldiers, have fought against al-Qaeda-linked fighters in northeastern Mali.
The attacks in the villages may also be an attempt to further exploit tensions between Tuareg and Fulani herdsmen.
“There have been 43 deaths in two days, all civilians, from the same community,” tribal leader Sidigui Ag Hamadi told AFP news agency from the regional capital, Menaka.
“Our fighters are destroying their bases and wiping them out. They are targeting innocent civilians,” he added, saying he viewed the bloodletting as a reprisal for attacks by armed Tuareg groups.
The Tuareg group National Movement for the Salvation of Azawad also put the death toll from the two attacks at 43.
It urged the governments of Mali and Niger to take steps to ensure that “an immediate end is put to these abominable crimes” and added that it would “not give in to any intimidation”.
Mali has been struggling with lawlessness in the north since Tuareg rebels and al-Qaeda-linked fighters sought to take control there six years ago.
Tuareg rebels declared independence in April 2012, just a month after President Amadou Toumani Toure was pushed out in a coup.
But three months later they lost ground to Ansar Dine, a group with links to al-Qaeda that imposed a strict interpretation of Islamic law on the local population, carrying out amputations and executions.
In early 2013, France intervened militarily to assist Malian government forces to take back the region.
Two years later, Mali’s government and Tuareg rebels signed a peace deal.
Speaking to Al Jazeera, analyst Nii Akuetteh said he believed the latest attacks were an attempt to provoke the Tuareg into a larger conflict.
“The Tuareg have had conflicts and disagreements with whichever government has been in Bamako ever since independence in 1960, because they, as a separate ethnic group, have always argued that they want to separate, they want their own country,” he said.
“They have always agitated for this. A few years back, they signed the most recent peace deal with the government which so far appears to be holding.
“[So,] why would the terrorists target them? It would seem that they are trying to get the Tuareg to once again pick up the guns and destabilise the government of Mali. I think that may be the reason why they are trying to target the Tuareg and get them fighting again.”