Zeid Ra'ad al-Hussein spoke during a three-day visit to the East African nation at the government's invitation. Ethiopian Prime Minister Hailemariam Desalegn has rejected United Nations and other outside requests to investigate the months of anti-government protests demanding more political freedoms.
The government has said at least 669 people were killed and largely blames the political opposition for the unrest.
Opposition figures and human rights groups say security forces killed protesters, while the government has called security forces' response "proportionate."
Zeid expressed alarm at the "extremely large number" of arrests and said some charges against those detained "may be misplaced."
He asked that UN staffers be allowed to visit the areas of unrest. "We may then perhaps provide a list to the government and ask for specific releases" of people detained, Zeid said. "This requires more attention."
The human rights chief also expressed concern about anti-terrorism laws in Ethiopia, saying that "an excessively broad definition of terrorism may be misused against journalists, bloggers and members of opposition parties."
Many civilians in Aburoc town, some of whom recently fled a military attack on nearby Kodok town, are ethnic Shilluk and have faced a sharp rise in government attacks as South Sudan's civil war continues.
Zeid said military commanders on both sides show little regard for protecting civilians.
Separately, the UN humanitarian affairs agency said roughly 100,000 civilians have been displaced after a South Sudan government offensive in the Jonglei region.
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