European children's agencies issued the warning in a report released in Amsterdam, where the EU's interior ministers were meeting to discuss how to deal with the influx of people fleeing war in Africa and the Middle East.
One of the main concerns is that EU countries, from Sweden to Britain, have implemented measures limiting family reunification rights — which risks separating children from their parents after they survive perilous journeys.
"It seems as if European countries are in a contest to win the title of 'least willing to accept asylum seekers,'" said the report from the European Network of Ombudspersons for Children, which represents 41 independent children's rights institutions in 34 European countries.
Last year migrant flows to Europe reached their highest level since World War II, with 1.2 million applying for asylum on the continent. The proportion of children rose from 26 percent in 2014 to 29 percent last year, the report said. Many were minors without their parents. In Sweden alone, 35,000 unaccompanied children requested asylum in 2015.
European leaders meeting in the Netherlands, which holds the rotating European Union presidency, are under pressure to balance the need to offer humanitarian shelter with widespread public opposition to admitting large numbers of newcomers.
The ministers will study an idea for a blocwide border and coast guard and discuss the looming expiration of temporary border controls reintroduced by several countries in Europe's passport-free Schengen travel zone.
The report also urged countries to improve transit and reception conditions, give children priority in the distribution of asylum seekers among the EU's 28 member states and set minimum standards of warmth and comfort at reception and transit centers.