In the eastern Trincomalee city, government offices, schools, shops and banks were shut and public transportation was halted.
Organisers said all communities joined in the protest in the multi-ethnic town as protesters burnt effigy of UN rights chief Navy Pillay and US President Barack Obama.
The protesters in Colombo called the proposed UN Human Rights Council resolution on Sri Lanka a gross interference in the country's internal affairs.
The UN Human Rights Council resolution, sponsored by the US, is the third in as many years on Sri Lanka's accountability and reconciliation with the Tamil minority after the end of the 37-year ethnic conflict.
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Sri Lanka has long resisted calls for an international investigation calling its own domestic processes were credible enough to deal with the allegations of civilian deaths.
The country's opposition blames the government for using the resolution for domestic political gain.
The government claims that President Mahinda Rajapaksa might be tried by the International Criminal Court. Demonstrations are meant to shore up public support for Rajapaksa.