Hailemariam told the BBC that an investigation by Ethiopia's Human Rights Commission was the only way to deal with the issue.
The Ethiopian prime minister (PM) rejected calls by the UN and EU for independent investigations into the deaths of hundreds of people during anti-government protests, over the past year.
PM Hailemariam Desalegn further stated that Ethiopia is able to carry out its own investigations.
Protesters from the Amhara and Oromia regions have been complaining about political and economic marginalization for months. This resulted in the government imposing a state of emergency aimed at halting the protests.
Ethiopia was overtaken by an unusually large number of demonstrations, which began in November 2015. International rights groups have said that hundreds of people have lost their lives in police-protester clashes. The Ethiopian Government has disputed the figures and said that the security forces were responding to "anti-peace forces."
Hailemariam told the BBC that an investigation by the Ethiopia's Human Rights Commission was the only way to deal with the issue. He pointed out that the commission was an independent institution, but admitted that it "lacked capacity" and could be strengthened. The prime minister also explained that the state of emergency had brought back "normalcy" to the country and added that those who were arrested are being held in prison and will face the judicial process.