Pope Francis concluded his two-day visit to Sri Lanka on Thursday and was seen off by Sri Lankan President Maithripala Sirisena before he left for the Philippines, an official said.

The President presented the Pope with an album containing the photos of his tour in Sri Lanka as a memento, an official said.

Pope Francis became the first pontiff to visit the former war torn northern region of Sri Lanka when he conducted a sermon on Wednesday to bless thousands and call for reconciliation.

On his second day the Pope flew by helicopter to historically the sacred Madhu shrine in the northwestern Mannar region, which operated as a neutral zone for thousands of refugees during Sri Lanka's three decade war with Tamil separatists.

In 1999 shelling killed 40 Tamil people who had sought refuge in the church and provoked global condemnation.

Thousands gathered at the shrine clapped and waved Vatican flags and the Pope made his way in an open pope-mobile.

Many hope that his visit will provide impetus to reconciliation between the Tamil minority and Sinhalese majority in the country.

"Only when we come to understand, in the light of the cross, the evil we are capable of and have even been a part of, can we experience true remorse and true repentance," he said after setting free a dove in a sign of peace.

The Pope has made reconciliation his key message during the two- day visit.

"There are families here today which suffered greatly in the long conflict," he said. "Many people, from north and south alike, were killed in the terrible violence and bloodshed of those years.

"No Sri Lankan can forget the tragic events associated with this very place... Here, in (the sanctuary), they feel safe," he added.

Earlier in the day over 500,000 people flocked to the shoreline of Sri Lanka's capital of Colombo to witness Pope Francis declaring Indian-born priest Joseph Vaz as the country's first saint.

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