Rajapakse assured Singh "all necessary measures" were being taken to keep civilians from harm's way in the battle with the Liberation Tigers of Tamil Eelam (LTTE), the Indian official said.
His call came a day after Indian Foreign Secretary Shivshankar Menon summoned the Sri Lankan ambassador to India, C.R. Jayasinghe, to discuss India's concerns.
On Friday, Sri Lanka also announced it would dispatch a delegation to India to defuse the mounting tensions between the nations over the conflict.
India directly intervened in the Sri Lankan conflict in 1987 by sending troops to supervise a bilateral peace pact, but ended up fighting Tamil Tigers.
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Singh conveyed his worries when Sri Lankan President Mahinda Rajapakse telephoned him to discuss "recent developments" in the country, the Indian leader's spokesman said in New Delhi.
Singh is under mounting pressure from Indian Tamil political allies of his ruling coalition to halt arms supplies to Colombo and mediate in the conflict between g