Miqdaad Versi, assistant secretary-general of the Muslim Council of Britain, the UK's largest umbrella group for Islamic associations, said he was aware of dozens of cases similar to that of the schoolboy.
"There are huge concerns that individuals going about their daily life are being seen through the lens of security and are being seen as potential terrorists rather than students," he said.
"This is a natural consequence of the extension of the 'Prevent Duty' to schools."
The Home Office does not publish data for the number of referrals made to Channel, the de-radicalisation programme.
However, in the year to the end of October, 1,355 people aged under 18 were referred to it, compared with 466 in the previous 12 months.
Police said the issue was reported to them but dealt with by a joint visit by a PC and social services.
"There were not thought to be any areas for concern and no further action was required by any agency."
The school said it was unable to comment because it was investigating a complaint made about the incident.