Some 275 homes were razed and 3,000 people forced to flee during a week of unrest in the south of the country, the National Bureau for Risk and Disaster Management said.
The violence was linked to widespread theft of prized zebu humped cattle, which sparked clashes between gangs of cattle thieves, known as "dahalos," villagers and the army.
A symbol of wealth, zebu are at the heart of local culture in the south of Madagascar, where they are eaten only at weddings or special celebrations, sacrificed for ancestor worship or in burial rituals.
Fatalities are common in Madagascar's zebu wars, which have fuelled inter-communal violence. The army has also been accused of carrying out extra-judicial killings and razing villages that are suspected of sheltering cattle rustlers.
Several security personnel have been killed.