School staff called police when a pupil looked at a UKIP website and an English Defence League video in class.
Mick Taylor said his 15-year-old son was asked by police whether he was a UKIP activist, and has described police action as inappropriate.
The procedure left him feeling "like a terrorist", Mr Taylor added.
Police said Wildern School in Hedge End, Hampshire, acted in line with safeguarding procedures. UKIP said: "We're certainly not extremists."
Under the new counter terror act, staff at schools are asked to identify children who may be influenced by extremist material.
The school said it called 101 for advice after a student was viewing a range of different sites and was referred to a specialist team.
"If my son had been accessing these websites on a regular basis - then maybe there would be cause for concern," Mr Taylor said.
"But it's a one-off incident and I don't think it merited such an extreme section of the police coming in."
Head teacher Marie-Louise Litton said: "I wish to make it absolutely clear that the decision to pursue the matter further was not made by the school."
A spokesman from Hampshire Constabulary said: "The school contacted us in good faith and in complete accordance with their safeguarding procedures.
"We have a duty to respond to these concerns and we spoke to the pupil and his father informally about comments and internet usage at school."
No further action was taken.
UKIP's deputy leader Paul Nuttall reacted angrily at the suggestion the party's website was flagged in this way.
"I don't know how you can be extremists when you have 22 MEPs, a member of Parliament, three lords and 500 councillors all over the country," he said.
"We're certainly not extremists."