At least 10,000 unaccompanied child refugees have disappeared after arriving in Europe, with many feared to have fallen into the hands of organised trafficking syndicates, Europol, the EU’s criminal intelligence agency said.

In the first attempt by law enforcement agencies to quantify one of the most worrying aspects of the refugee crisis, Europol’s chief of staff Brian Donald told the Observer that thousands of vulnerable minors had disappeared since registering with authorities.

At least 5,000 children have gone missing in Italy alone, Donald said, adding that another 1,000 have vanished in Sweden.

Donald warned that a sophisticated pan-European “criminal infrastructure” was now targeting refugees.

“It’s not unreasonable to say that we’re looking at 10,000-plus children. Not all of them will be criminally exploited; some might have been passed on to family members. We just don’t know where they are, what they’re doing or whom they are with.”

Moreover, there is already evidence of sexual exploitation, especially in Germany and Hungary. “An entire [criminal] infrastructure has developed over the past 18 months around exploiting the migrant flow. There are prisons in Germany and Hungary where the vast majority of people arrested and placed there are in relation to criminal activity surrounding the migrant crisis,” said Donald.

Thickening the plot, Police have discovered that the illegal gangs helping refugees come to the EU are the same gangs involved with human-trafficking. “The ones who have been active in human smuggling are now appearing in our files in relation to migrant smuggling,” said Donald.

The fate of unaccompanied children refugees is becoming a major concern in the EU, as the number of missing minors swells. Last week it was announced that Britain would accept more unaccompanied minors from Syria and other conflict zones. According to UK charity Save the Children estimates, a least 26,000 lone refugee children entered Europe in 2015. It has recorded multiple cases of sexual abuse, violence, and extortion involving child refugees and is calling on the UK to resettle 3,000 of them as soon as possible.

“These children need and deserve our help and protection. Left to fend for themselves, lone children are extremely vulnerable along the refugee route. Children report having been beaten, extorted, and sexually abused on their journey,” Save the Children CEO Justin Forsyth said.

Meanwhile, Europol estimates that 27% of the refugees that arrived in Europe in 2015 were minors.

“Whether they are registered or not, we’re talking about 270,000 children. Not all of those are unaccompanied, but we also have evidence that a large proportion might be,” said Donald, indicating that his estimate of 10,000 missing child refugees is likely much too low.

Europe’s chaotic approach to the migration crisis led last week to calls for Greece to be removed from the open-borders Schengen zone, a development that a senior UN official has described as a “new nadir” in the EU’s approach.