Sri Lanka's Prime Minister, who oversaw a brutal end to a decades-long conflict with Tamil separatists, said on Wednesday the country was withdrawing from a United Nations resolution investigating alleged war crimes.

Mahinda Rajapaksa was president when Sri Lankan troops defeated Tamil Tiger rebels in 2009, but rights groups accused the army of killing at least 40,000 civilians in the final months of the conflict.

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His brother Gotabaya, who is now president, was defence secretary at the time.

Prime Minister Mahinda said the government would no longer abide by a 2015 resolution calling for accountability for alleged excesses carried out by Sri Lankan troops and reparations for victims.

Sri Lanka co-sponsored the resolution at the United Nations Human Rights Council along with 11 other countries calling for the investigation of allegations of wartime atrocities by both government forces and the Tamil Tiger rebels, who were fighting for a separate homeland for Sri Lanka's ethnic Tamil minority.

Mahinda's announcement comes days after the US State Department imposed a travel ban on Sri Lanka's army commander, Shavendra Silva, and his family over alleged human rights violations in the final stages of the civil war in 2009.

Historic betrayal

He said Washington's recent decision to ban the army chief was because Colombo had signed up to the resolution.

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"It is because of the historic betrayal ... in co-sponsoring UN Human Rights Council Resolution 30/1 in 2015 that other countries are able to name members of our armed forces as violators of human rights," he said in a statement.

Before winning the presidency, Gotabaya had pledged he would not honour the previous government's commitments to the UN.

According to a 2015 report by the office of the UN high commissioner for human rights, Silva had been tasked with freeing Puthumattalan, one of the last strongholds of the now-defeated Tamil Tiger rebels.

The investigation cited witnesses as saying the army unit he was leading shelled a hospital and a UN hub.

Silva has denied targeting hospitals in his statement to a government-appointed commission, saying that the facility was being used to treat rebel fighters, the report said.

Foreign ministry officials could not be immediately reached on Wednesday for comment on Rajapaksa's announcement.

Mahinda's administration was on the verge of international sanctions because of its refusal to investigate the alleged war crimes when he was defeated at the January 2015 elections.