Militants on motorbikes overwhelmed the villages simultaneously on Sunday evening, entering and killing indiscriminately and burning and ransacking homes, according to security officials.
"The terrorists went into the villages and massacred everyone," a military officer told AFP, speaking on condition of anonymity. "More than 40 civilians were killed by terrorists on Sunday in the villages of Karou, Ouatagouna and Daoutegeft," they said.
A Malian army patrol was sent to the affected communities on Monday. The death toll confirmed by the patrol was at least 51, according to Reuters.
"Provisional toll is 51 killed, several others injured," read a note from the local district administrator to the Gao regional government in south-east Mali.
Another local official, who also spoke on condition of anonymity said "20 civilians were massacred in Karou. Fourteen civilians were killed in Ouatagouna, and other civilians were killed in the hamlet of Daoutegeft."
The attacks in Mali mark the latest in a wave of deadly attacks to have beset the Sahel region in West Africa, where largely impoverished civilians in Burkina Faso and Niger have experienced constant violence for almost a decade.
Last Wednesday, 30 people including 11 civilians and 19 security personnel were killed by suspected jihadists in northern Burkina Faso.
Armed groups linked to al-Qaida and the Islamic State terror group have launched attacks since 2012 in Mali, Burkina Faso and Niger.
The security crisis began with unrest in northern Mali in 2012, when President Amadou Toumani Touré was overthrown by a military uprising. Militants seized on a power vacuum, leading an insurgency that has exploited ethnic grievances across the Sahel, as well as poor governance, corruption and poverty.
The military of the former colonial ruler, France, as well as the UN peacekeepers and other European forces alongside the Malian army, have battled the insurgents, recording gains at the onset of the crisis. Yet in recent years, attacks have soared.
Thousands of civilians and troops have died, with millions in need of humanitarian support. More than 380,000 people have been displaced, fleeing their homes in northern and central Mali, with two-thirds of them children. In neighbouring Burkina Faso, more than 1.3 million have been internally displaced, in a rapidly worsening humanitarian crisis.
The presence of the so-called Barkhane military operation of about 5,000 soldiers, has grown more controversial in recent years, as violence has continued to spread in the Sahel. Civilian casualties blamed on French forces have fuelled local grievances and international criticism.
Comment: The West's 'help' in the region is beginning to look a lot like their interventions in the Middle East: French air strike on wedding in Mali killed 19 civilians, violated international law - UN
France has said it will dramatically reduce its forces by the end of next year, which has also sparked concern in regional governments, that the insurgency will grow more deadly without further support.