Two Orthodox churches in Shirka district fell under fire Saturday, with witnesses saying homes were burned and bodies found in the rubble.
Oromia, Ethiopia's largest state, has long been a tinderbox of ethnic and religious conflict, with insurgent groups exploiting faith divisions to rally support.
The Ethiopia Human Rights Commission said it was monitoring the situation, while a deacon from one of the hit churches appealed for swift governmental intervention.
Security officials have mobilized to investigate the attacks, warning that unchecked violence could trigger a wider crisis across the Horn of Africa.
One priest, who requested anonymity, said his congregation mourns the loss of 46 souls, including his own brother, and fears further reprisals.