The news emerged as charity Save the Children estimated that around 26,000 migrant children were forced to travel into Europe alone last year.
Brain Donald, Europol's chief of staff, told Guardian’s Observer: 'It is not unreasonable to say that we are looking at 10,000-plus children. 'We just don't know where they are, what they are doing and whom they are with.'
He said there was evidence some were being sexually exploited by gangs also linked to human trafficking, but stressed not all children would have been linked to criminal activity.
Mr Donald added that the abuse was not happening 'in the middle of forests' but in towns and built-up areas.
"UNICEF told Mail Online that there are as many as 90,000 unaccompanied minors in Germany and Sweden alone, and more than one in three migrants in Europe are children."
He said: 'These kids are in the community, if they're being abused it's in the community.'
A spokesman for UNICEF said that protection systems in Europ are inadequate so many are being 'exposed to abuse and exploitation' - and traffickers will 'abuse their vulnerability' as border policies tighten.
A spokesman for Unicef said: 'The UK has a responsibility to protect vulnerable migrant children, it is absolutely right that the government is committed to resettle unaccompanied children from conflict regions.'
The crisis in Syria and unrest in some parts of the Middle East, North Africa and beyond have separated a large number of refugee children from their families.