In a video message to the council, Pillay reiterated concern over allegations that Tamil rebels prevented civilians from fleeing the combat zone and used them as human shields.
She also highlighted reports that the government fired heavy artillery on the densely populated area, and claims that the army may have killed rebels who were trying to surrender.
Pillay said ensuring accountability for abuses committed would be important for the nation's reconciliation.
But Dayan Jayatilleka, the Sri Lankan ambassador, said it was "outrageous" to suggest the government be investigated.
Pillay's comments come as the UN Human Rights Council tries to reach consensus on their approach to the aftermath of the conflict, with two separate draft resolutions tabled for UN special session.
On one side, a Western-led group is demanding unrestricted access to around 300,000 Tamil civilians said to be forcibly held in government-run camps, and also calls for an inquiry into allegations of war crimes.
The other resolution, backed by Sri Lanka and its allies, praises its government for liberating Tamil civilians and its humane treatment of those displaced.
Sri Lanka declared total victory over the LTTE a week ago after killing their leaders.
The UN estimates that up to 100,000 people died during the 26-year conflict, including at least 7,000 civilians killed since the beginning of the year.