A Europol spokesman said the names of some suspected migrant smugglers are also appearing in the agency's human trafficking database -- indicating some of those missing might be vulnerable to trafficking.
Leonard Doyle, spokesman for the International Organization for Migration, said he was appalled by the figure.
"We think it's shocking that we are now learning that there are so many unaccompanied minors exposed to trafficking and other dangers," Doyle said.
"That is another tragic twist in the latest story of migration to Europe and the need to protect vulnerable young people who find themselves at loose without friends in Europe and therefore vulnerable without proper mentoring and leadership."
More than 1 million migrants entered Europe last year. Many are refugees from Syria, where civilians grapple not only with a gruesome civil war but also the threat of ISIS. Others came from elsewhere in the Middle East and North Africa, trying to escape poverty and persecution.
But thousands who attempted the journey across the Mediterranean Sea didn't make it. Read more on edition.cnn.