HRW claims the Ethiopian federal forces have committed atrocities in 13 towns with a population of 23 million people, together with a government-affiliated militia.
One of the three was shot dead, a second died of his wounds in hospital while the third was arrested, the statement said.
The NGO called for the suspension of all deployments of Ethiopian federal forces to peacekeeping missions until "commanders responsible for grave abuses are held accountable."
Government officials in Addis Ababa have said on several occasions that the violence in Amhara, the second largest region in Ethiopia, is under control.