"The last thing India would want is an influx of refugees to its territory," G Parthasarthy, a former Indian diplomat and expert in Indo-Sri Lanka relations said.
Thousands of refugees have poured across the narrow Palk Strait into Tamil Nadu repeatedly since the war started in 1983.
Singh last month refused to meet Rajapaksa at the United Nations General Assembly in New York, which analysts say was a sign that he was unhappy with the progress of political negotiations on the Tamil issue.
Rajapaksa's government has promised that devolution for Tamil areas in the north and east of the island would go hand-in-hand with its push to win the war.
"A year ago the President had given repeated assurances that while the military component was going on, he would have a political package ready," Colombo-based analyst Iqbal Athas said. "The fact that process has not moved forward is why Singh didn't give him an appointment in New York."
It also prompted Rajapaksa to call a meeting of the All Party Representative Committee (APRC), a panel designed to forge a political compromise, over the weekend and urge the Tigers to lay down their weapons and enter the democratic process, Athas said.
A senior Sri Lankan government official said Rajapaksa's offer was not too different from the solution Singh had demanded.
"The government agrees that the concerns of the minority must be addressed through a political process, which is already on train," the official said on condition of anonymity, referring to the APRC.