Mark Rowley, assistant commissioner for specialist operations at the Met Police and head of the UK's national counter-terrorism policing, said in many cases children seen at fear of radicalisation were taken into social care.
"The most extreme cases that end up with children being made wards of courts or care proceedings is real tricky stuff because we've never had to deal with national security issues before in a family court. We had never done [a case] before 2015 but the fact that it's [now] into 40 or 50 cases is illustrative of the scale of the problem," Rowley told 'The Sunday Times' in an interview.
Some of the cases involved infants and young teenagers who had been made wards of court after their parents tried to take them to Syria to join terrorist groups, the report said.
More than 700 British people are believed to have travelled to Syria and Iraq to join groups such as Islamic State (ISIS) since 2014 but the figure is now on the decline.
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"So we intercept them now, but we don't see that interception as a solution in itself. It's the start of solving it," he said.
Rowley said Scotland Yard was "closing" about 50 investigations a month into young people who had been thought at risk of radicalisation and praised the greater willingness of teachers and social workers to alert police to their suspicions about youngsters.
His interview comes a week after Neil Basu, the Indian-origin deputy assistant commissioner at the Met, had said that 10 terrorist plots had been foiled in the past two years and the security services are tackling 550 "live" cases at any one time.