Navi Pillay, speaking at the end of a controversial fact-finding mission to assess Sri Lanka's progress after the 26-year war between the government and separatist Tamils, said she was "deeply concerned" about the situation.
She said: "It is important everyone realises that although the fighting is over, the suffering is not.
"I'm deeply concerned that Sri Lanka, despite the opportunity provided by the end of the war to construct a new, vibrant, all-embracing state, is showing signs of heading in an increasingly authoritarian direction."
Pillay said reconstruction and redevelopment are important achievements in former war zones, but added: "Reconstruction alone will not bring reconciliation, dignity, or lasting peace."
She also said she was concerned about the degree to which the "military appears to be putting down roots and becoming involved in what should be civilian activities, for instance education, agriculture and even tourism".
The UN says at least 40,000 Tamil civilians were killed by Sri Lankan government forces in the final stages of the civil war, which ended four years ago.
A Channel 4 investigation in 2011 revealed a litany of war crimes towards the end of the conflict, including soldiers raping Tamil women, the systematic execution of naked, bound prisoners-of-war, and the strategic denial of food and medicine to hundreds and thousands of trapped civilians.
A UN panel has said it has "credible allegations" that both sides committed atrocities and war crimes, and singled out the government for most of the blame.
Sri Lankan president Mahinda Rajapaksa told the UN High Commissioner for Human Rights that his people believed the UN is a biased organisation.
Sri Lanka has come under international pressure to bring to book those accused of war crimes. The regime has rejected the accusations of rights abuses, although Rajapaksa last month ordered an inquiry into mass disappearances.