At least 11 people were killed in the attack in Igangan in Oyo state late on Saturday, police said.
Violence is increasing against a backdrop of poor governance and deteriorating socio-economic conditions in northern Nigeria, further exacerbating instability across the region.
The fighting took place on Friday and Saturday in Salamat province, after cattle belonging to one herder ruined a field. The herders attacked as the farmers were taking the animals into an enclosure.
The Mali-based United Nations mission, MINUSMA, reports "an increase in serious human rights violations attributable to the Malian security forces."
Officials say attack targeted a Fulani village in volatile Mopti region where Fulani herders and Dogon hunters occasionally clash.
HRW interviewed 17 people over the alleged killings, including 12 witnesses to the arrests and later burial of the victims, in Djibo, about 200 kilometres north of the capital Ouagadougou.
Thirty-one people – mostly Fulani herders – were apparently killed by Dogon hunters, a local official says. Nine soldiers were killed in a separate attack in central Gao region.
Twenty-one people were killed in an attack overnight in Ogossagou village while the rest died in separate attacks.
Armed men on motorbikes, wearing garb of traditional hunters known as Dozo, attack Siba village in central Mali, killing 13 men and one girl, UN says.
UN human rights office spokeswoman Ravina Shamdasani says last weeks "horrific attacks" signal a "spike in killings" in a cycle of violence in the region that has caused 600 deaths and displaced thousands since last March.
Attackers dressed as traditional Dogon hunters targeted Fulani herders in the villages of Ogossagou and Welingara in Mopti region, officials say.
Mostly young men were killed in two attacks in northern Menaka region, which seem calculated to spark an ethnic conflict between Tuareg and Fulani herders, governor Daouda Maiga says.
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