The two countries were set to sign an agreement to lease out oil tanks to India to jointly operate a strategic oil facility in the eastern port district of Trincomalee.
But Sri Lanka's opposition parties have objected to the deal, saying the government was selling state assets to India.
"The information I have is that all deals have already been signed. So the Indian prime minister's arrival or non- arrival would be immaterial," Rajapaksa told reporters in the central town of Kandy, hours before Modi touched down in Colombo.
"The problem will be only if they sign agreements. I understand these have already been signed," he said.
According to the proposed deal, at least 73 of the 99 storage tanks in Trincomalee is to be managed under a new equity arrangement between India and Lanka. In 2002, the Indian Oil Company was given 14 of the 99 tanks to operate.
Modi is primarily in Sri Lanka to participate tomorrow in the International Vesak Day celebrations, the biggest festival of Buddhists. This is his second visit since Rajapaksa's unexpected defeat in 2015 polls by Maithripala Sirisena.
"I will take part in the UN Vesak Day, my going there will not mean I have gone to welcome the Indian prime minister," said the Sinhala strongman who ruled the country for a decade.
Rajapaksa's joint opposition has led a resistance to the Sririsena government's plan to enter into economic cooperation pacts with India, more particularly the Trincomalee venture.
The state petroleum workers last month led a crippling work stoppage to protest the deal.
Ahead of Modi's visit, Sirisena had slammed what he termed the opposition's misinformation about the visit. He said Modi's visit was restricted to the Vesak Day celebration hosted by Colombo.
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