Rajapaksa is set to meet the two leaders on September 20, External Affairs Minister G L Peiris told reporters here today.
Rajapaksa is travelling to Sanchi in Madhya Pradesh on September 19 to lay the foundation stone for the construction of a Centre for Buddhist Studies.
The meeting with the Indian Prime Minister would be the first for Rajapaksa since India voted in favour of the anti-Sri Lanka resolution that censured the nation over its human rights record at the UNHRC sessions in Geneva in March.
The resolution said that Sri Lankan troops deliberately targeted civilians during the last phase of the civil war with the LTTE which ended in 2009.
Although Sri Lanka-India relations have been rekindled since the passage of resolution with a number of high-profile visits to country by Indian dignitaries, the recent events which reflected anti-Sinhala sentiments in Tamil Nadu have muddied the waters.
A parliamentary delegation led by Sushma Swaraj, the opposition leader in the Lok Sabha, visited the country in April. External Affairs minister S M Krishna visited Colombo prior to Swaraj's delegation.
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Tamil Nadu Chief Minister Jayalalithaa has been urging the Centre to curtail training for visiting Sri Lankan defence officials in the state. She also ordered the return of a Sri Lankan football team.
Following attacks against a group of Sri Lankan Catholic pilgrims in Chennai, Sri Lanka issued a travel advisory warning against travel to the Indian state.
Last week, Rajapaksa had said the Indian government responded positively to his country's request to guarantee the safety of its citizens and only a small, politically-motivated group was responsible for the harassment.