But worryingly, she said that the number is probably even higher as authorities have no clue where the children have gone, who may have taken them, or what is being done to them.
It has stoked fears that the children could be exploited by human traffickers or radicalised by Muslim extremists.
Ms Wikstrom, Chair of the European Parliament Petitions Committee, admitted that thousands of adult asylum seekers also “go missing” each year once they arrive in Europe.
Last year, Germany admitted that it had lost tack of over 130,000 asylum seekers, according to its Government’s figures.
German chancellor Angela Merkel said authorities could not find 13 per cent of the 1.1 million people registered as asylum seekers last year.
Swedish Liberal MEP, Cecilia Wikström is carrying out reforms on the Dutch regulations
And this is why the EU is urgently unveiling a raft of proposals to keep better track of asylum seekers by making them register as soon as they arrive.
Ms Wikstrom insisted the EU did its “utmost to stop secondary movement” referring to migrants moving after being placed somewhere, before going under the radar.
Thousands of adult asylum seekers also “go missing” each year once they arrive in Europe.
And when pressed on whether she knew where the missing asylum seekers were, she said: “If Europol don’t know where the children are, I don’t know either.
“They could be being abused. They could have been trafficked. We just don’t know. We don’t know where they are.”
Ms Wikstrom advised that urgent changes need to be made so that European authorities can begin to “register [the asylum seekers] and follow them”.
Meanwhile, the UK is also grappling with the loss of hundreds of child refugees, according to The Independent.
German chancellor Angela Merkel said it could not find 13 percent of the refugees
It claimed that over the past five years 9,287 children came to England as an “unaccompanied minor” alone, without a parent or guardian.
But 360 have gone missing and are still unaccounted for.
Ms Wikstrom, who today launched plans to overhaul the EU asylum system, said: “What we are facing today is a new situation. We need to profoundly change the current asylum policy in Europe.”