A legal campaign by a pair of 13-year-old twins has forced police chiefs to admit carrying out unlawful stop and searches on thousands of climate change protesters.

The twins won a high court battle against the police after one of them was left "crying and shaking" and fearing that he would go to prison for having a sticker in his bag.

As a result of their victory, police have been compelled to apologise after 3,500 climate protesters at the Kingsnorth power station in Kent were stopped and searched at airport-style checkpoints at the demonstration.

Adrian Leppard, Kent police's acting chief constable, admitted that the protesters' human rights had been breached.

The admission is the latest embarrassment for the force, which has been heavily criticised over its £5.3m operation to control the week-long demonstration against a proposed coal-fired power station at Kingsnorth two years ago.

Kent police have faced allegations of brutality by officers who concealed their badges and used loud music to prevent camapigners sleeping.

The twins, who cannot be named, and Dave Morris, another activist, have each been awarded more than £1,000 compensation after they took Kent police to the high court. More than 40 other Kingsnorth demonstrators are pursuing legal action against the force.

One of the twins, a boy, said: "I had stickers and stuff that I was scared about. When I was in the queue I heard stories about people being searched and taken away. I was worried that they would arrest me too because of the stickers."

The other, a girl, said: "We arrived at the protest ourselves and we then tried to meet up with our mum. There was a long line of people waiting to be searched, and it was a bit scary. It was really unfair – we weren't actually doing anything.

"It made me more wary of police. Before I just thought they were there to help us if we have problems. It was like they were above the law. We're trying to change the world for them as well, not just us."

Their solicitor, John Halford, said it was very worrying that "violation of human rights to protest on a massive scale" had been exposed not by two internal police investigations but by "two tenacious children" and an activist.

Police searching the protesters were required to have a reasonable suspicion that an individual was carrying prohibited weapons that could be used for criminal damage, according to the 1984 police and criminal evidence act.

However a secret document, disclosed by Kent police at a late stage in the litigation, showed that police officers had instead adopted a blanket approach.

Kent's assistant chief constable Andy Adams said their policing of the Kingsnorth demonstration "was very successful in preventing criminality and harm, while at the same time enabling a protest around an issue of genuine public concern to go ahead".

As part of the settlement, Kent is required to write to all police forces explaining what happened to ensure that protesters are not unlawfully searched under the act in future. In the letter, Kent's chief constable will say: "Many people were searched as a result of these briefings. That should not have happened.

"I accept that the combination of the act of stopping and searching these individuals breached their rights under articles 8, 10 and 11 of the European convention on human rights and lessons must be learned."