He was speaking after around 668 migrants and refugees were saved from boats in the Mediterranean off Libya on Saturday.
They were rescued by Italian coast guard and navy ships, aided by Irish and German vessels and humanitarian organisations, Italian and Irish officials said.
The UN refugee agency says more than 700 migrants may have drowned in the Mediterranean Sea south of Italy in the past few days as they tried to reach Europe, the UN refugee agency said.
Carlotta Sami, spokesperson for UNHCR, said an estimated 100 people are missing from a smugglers' boat that capsized on Wednesday.
She said about 550 others are missing from a smuggling boat that capsized on Thursday morning.
Refugees said that boat, carrying about 670 people, did not have an engine and was being towed by another smuggling boat before it capsized, Ms Sami added.
About 25 people from it survived, 79 others were rescued by patrol boats and 15 bodies were recovered.
Ms Sami said 45 more bodies were recovered from a shipwreck on Friday and many more are reported missing.
Speaking at the Vatican on Saturday, Pope Francis told several hundred children, including many from abroad, who came from the Italian south to see him, that migrants and refugees "aren't a danger but they are in danger".
The pontiff held a red life vest, given to him recently by a volunteer, and told the children it was the vest used by a Syrian girl who died while trying to reach the Greek island of Lesbos.
He told the children: "She's in heaven, she's watching us."
The is not the first time Pope Francis expressed his disappointment that some European nations have refused to accept migrants and refugees fleeing poverty or war.
He has criticised countries building fences and other barriers to stop the arrivals from journeying northward after reaching the continent's southern shores.
In April the Vatican said that the pope would taken in 12 refugees after his visit to the island of Lesbos.
Under a European Union deal, tens of thousands of those rescued at sea and seeking asylum were supposed to be relocated to other EU nations from Italy and Greece, whose shores have received most of the arrivals in recent years.
But with resentment building in some European countries about taking in outsiders only a small percentage have actually been moved.
Most recently Greece has been publicly criticised for rehousing thousands of migrants in camps unfit for purpose.