Canada's Prime Minister Stephen Harper has threatened to withdraw funding for the Commonwealth in an escalating row over rights abuses by Sri Lanka ahead of a summit next month.

Harper confirmed late Monday that he was boycotting the November 15-17 summit in Colombo, citing "the absence of accountability for the serious violations of human rights" during and after Sri Lanka's long civil war against Tamil separatists.

"I do this with somewhat of a heavy heart. This is a great disappointment," he told reporters at an Asia-Pacific summit on the Indonesian island of Bali, while stressing that Canadians were "absolutely overwhelming" in their view that he should stay away.

Sri Lanka's government had shown a "considerable worsening" over the past couple of years in terms of democratic governance, post-war reconciliation and respect for human rights, Harper said.

He added that "obviously we will examine our engagement and our financing of the Commonwealth, which is quite considerable, to make sure that we are wisely using taxpayers' dollars and reflecting Canadian values".

After Britain, Canada is the second-largest contributor to the Commonwealth budget, providing about $20 million last year.

In August, UN human rights chief Navi Pillay raised fresh concerns for the safety of journalists and activists she met during a week-long fact-finding mission to Sri Lanka.

She left the island arguing that democracy had been undermined and rule of law eroded in Sri Lanka four years after the end of its bloody ethnic war, which by UN estimates claimed up to 100,000 lives between 1972 and 2009.

The UN has reported "credible allegations" that up to 40,000 civilians were killed in the final months of fighting against the Tamil Tigers which ended in May 2009. Sri Lanka has rejected the charges and maintains that its troops did not kill a single civilian.

Harper's remarks further clouded the buildup to the Colombo summit after Gambia announced last week that it was pulling out of the Commonwealth, whose roots lie in the former British Empire, saying it would "never be a member of any neo-colonial institution".

But Australia's new Prime Minister Tony Abbott, who met Harper in Bali on Monday, said he does intend to go the summit despite the calls for a boycott from Human Rights Watch among others.

"You do not make new friends by rubbishing your old friends or abandoning your old friends," the pro-monarchy Abbott said, referring to Australia's ties to the bloc as a whole, vowing that his government would "take the Commonwealth seriously".

Others including British Prime Minister David Cameron are also expected to attend the gathering of the Commonwealth, which is headed by Queen Elizabeth II. Prince Charles is expected to deputise for his mother in Colombo.