Sri Lankan Prime Minister Ranil Wickramasinghe was present at the Colombo airport to see-off Modi.
On the last day of his five-day three-nation tour that also took him to Seychelles and Mauritius, Modi became the first Indian prime minister to visit Jaffna. The prime minister, who is also the second international leader to visit the once strife-torn region after Premier David Cameron in 2013, handed over 27,000 new homes to Tamils who became homeless during the civil war.
During his Sri Lanka visit, Modi reached out to the country, saying the security of the two nations is "indivisible" and favoured a life of equality, justice and dignity for Tamils in its "new journey" of peace and reconciliation.
The first prime minister to visit the island after Rajiv Gandhi's trip in 1987 following which the bilateral relationship had undergone several twists and turns, he said the two nations should build a climate of trust and confidence while remaining sensitive to each other's interests.
He addressed the Sri Lankan Parliament and held talks with the top Lankan leadership, including President Maithripala Sirisena, during his visit.
Modi had started his trip on Tuesday when he reached Seychelles and held talks there, signing four agreements.
He then went to Mauritius where he met the leadership of the strategic Indian Ocean island. India and Mauritius signed five pacts during Modi's visit.
The prime minister also addressed the country's National Assembly and attended a public reception.
Modi's final destination was Sri Lanka and during his trip to the islanad, Modi visited Colombo, Sri Lanka's ancient capital Anuradhapura, Talaimannar and Jaffna.
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