Rajapaksa says his election defeat was a conspiracy as parliament prepares to debate bill limiting presidential powers.
The US secretary of state has said he wants to renew ties with Sri Lanka and urged its new government to work with the UN to ensure an investigation into war crimes met international standards.
John Kerry arrived in Sri Lanka on Saturday, the first time in a decade that a US secretary of state has visited Sri Lanka.
He announced the start of an annual bilateral dialogue and said the US would immediately send experts to advise the new government on economic growth, trade and investment.
“Kerry spoke frequently about the need for the citizens of this island country to not forget their past, and to find a way to reconcile their past grievances,” Al Jazeera’s Rosiland Jordan, reporting from Colombo, said.
“In Sri Lanka, that means squaring political, ethnic and religious differences. It also means trusting each other, something that can’t be legislated.”
Kerry’s visit comes after years of tensions between the US administration and Mahinda Rajapaksa, the former president, over allegations of human rights abuses and war crimes at the end of a long conflict with Tamil separatists, which ended in 2009.
Rajapaksa was unseated by Mathripala Sirisena in a surprise election win in January.
Rajapaksa’s government had also clashed with the UN over its investigation into war atrocities.
At Sirisena’s request, the UN has agreed to delay its report until September.
In a speech to business leaders and activists in Colombo, Kerry said it was important that the new government cooperate with the UN and mount an investigation seen as legitimate within Sri Lanka.
He said a process of reconciliation was needed to heal the wounds of more than two decades of war.
Kerry also urged the government to release all remaining political prisoners and work with international organisations to investigate missing persons cases.
“Sri Lanka is at a pivotal point. Peace has come but true reconciliation will take time,” Kerry said.
Kerry briefly met Sirisena and later Ranil Wickremesinghe, the prime minister.
He was expected to meet R Sampanthan, who heads the main ethnic Tamil political party, on Sunday before going on to Kenya for his next stop.
Kerry said the US was not seeking to meddle in Sri Lanka’s internal affairs.
“Everything we are talking about, we are offering, not demanding, everything we have suggested is exactly that, a suggestion,” he said.
Rajapaksa had also established strong ties with China during his term.