Schools are referring to the police record numbers of pupils and staff identified as being at risk of radicalisation.

Official data to be released on Tuesday will show that the details of 1,281 people were referred to the government's Channel scheme, up from 748 the year before, with officers citing the civil war in Syria as the main reason for the increase.

Sir Peter Fahy, the chief constable of Manchester police who leads on extremism for the Association of Chief Police Officers (Acpo), told the Guardian that schools were now the greatest source of concern for the police, followed by local authorities, the NHS and then higher education.

But he said people should not be surprised that "Muslim lads" felt compelled to travel to Syria after seeing in the media the atrocities committed there.

Since 2007, 1,450 children aged 18 and under have been referred to Channel, which provides early intervention support to people at risk of radicalisation, the Acpo figures show.

The disclosure that education is at the forefront of anti-terror measures comes in the wake of the Trojan Horse scandal, in which Ofsted and the Department for Education placed five schools in inner-city Birmingham into special measures.

Fahy defended Channel and the overarching Prevent strategy, which aims to stop people becoming terrorists or supporting terrorism, saying it was "just trying to look out for vulnerable young people and to try and avoid using a criminal justice intervention".

He said: "It's been a difficult issue with some of the people we know who have been wanting to go to Syria and the people who have come back. Do you want to prosecute them? We have stopped young people on the way to the airport going to Syria. They have not been prosecuted but instead we are working with other agencies to get them help."

Fahy risked criticism from some quarters by adding: "We all feel desperate about Syria. I have written to my MP. I have watched those reports about Aleppo and Homs and say: 'What the hell can I do?' Don't be surprised that Muslim lads look at that and say: 'What the hell can I do but go out there and help them.'"

In 2011, the government redefined the counter-terrorism programme and asked public officials such as doctors and teachers to help identify people who were "vulnerable to being drawn into terrorism". Campaigners complained that this was in effect creating a surveillance state that "spies on Muslims".

Asim Qureshi, research director of Cage, an advocacy group that campaigns against measures introduced in the wake of the war on terror, said: "The problem is that the indicators used to identify what the government calls extremism are often opinions or beliefs held by the vast majority of practising Muslims in this country. Therefore, for many Muslims, Prevent appears to be a policy aimed at criminalising Islam.

"We've come across cases where people feel that they have been referred simply because they hold certain perfectly legal views, such as about foreign policy, or that they have decided to grow a beard or wear a niqab. Conflating legitimate viewpoints or religious symbolism with a propensity to commit violence displays a worrying lack of nuance in the government's engagement with the Muslim community, and can only serve to alienate people further."

• This article was amended on 15 July 2014. An editing error led to an earlier version saying that the figures were for referrals to Prevent, rather than to Channel.