Malcolm Ranjith, the archbishop of Colombo, urged President Mahinda Rajapaksa and the main ethnic Tamil party to thrash out a political settlement or risk an international investigation.
"Foreigners should not tell us what to do...We are not a pack of fools," the cardinal said. "But if we do not resolve these issues, then we open ourselves to foreign intervention."
He said without letting foreign countries to interfere Sri Lanka's government ought to make a genuine effort to implement recommendations of its own Lessons Learnt and Reconciliation Commission (LLRC).
We tell the world please do not interfere in our country. But we cannot remain without resolving our problems by telling the international community not to interfere, he said.
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Sri Lanka has often cited the LLRC as its own mechanism when faced by international calls to establish an independent investigation into alleged war crimes for which a UN special panel had held both the government and the LTTE responsible.
In a 24-page pastoral letter, the church warned that Sri Lanka's failure to ensure accountability for alleged war crimes could trigger international investigations that will be a "serious threat to the sovereignty of the country".
Christians are a small minority in the Buddhist majority Sri Lanka, but the Catholic church wields considerable influence over the government.
Since the end of the ethnic conflict with the Tamil separatists in 2009, Sri Lanka has faced accusations of ignoring international calls for accountability over alleged 40,000 ethnic Tamil civilians deaths.
Two successive resolutions in the UN rights body were adopted against Sri Lanka. The US-moved resolutions, which were backed by India, urged quick action to implement the LLRC recommendations.