The Home Office has been forced to make it clear that anti-fracking campaigners should not be considered extremists after a council and a school in North Yorkshire used the government’s counter-terrorism programme to target environmental protesters.

City of York council included anti-fracking activists in its Prevent programme, the controversial centrepiece of the government’s strategy to tackle extremism and thwart terrorism. In response, the Home Office on Saturday issued a statement saying “support for anti-fracking is not an indicator of vulnerability” to extremism.

The council had placed anti-fracking protesters on a list of “key risks to York”, along with Islamic terrorists and far-right extremists. And an East Yorkshire secondary, Driffield school, was condemned for including anti-fracking campaigers in its counter-terrorism advice for parents.

The information commissioner recently backed the decision by five police forces – Cheshire, Cumbria, Greater Manchester, Lancashire and Merseyside – to refuse to release data about the number of people they viewed as allegedly at risk of being drawn into extremism through their involvement in anti-fracking campaigns.

The use of Prevent’s powers to target anti-fracking campaigners has prompted renewed criticism that the counter-terrorism programme is seriously flawed.

Amrit Singh, senior legal officer at the Open Society Justice Initiative, said: “This is yet another sign that Prevent is structurally flawed and in dire need of independent review and reform. It is a clear example of how Prevent’s sweeping definition of extremism threatens the very British values it seeks to uphold, by penalising free expression on issues vitally important to the public.”

In October the initiative released a detailed report claiming that Prevent presented a serious risk of human rights violations and was so flawed it was counterproductive.

Fiyaz Mughal, director of anti-extremism group Faith Matters, said: “This is a direct attack on democratic opposition and a direct attack on dissent against the state. News that fracking protectors are being lined up with IS- [Islamic State-] inspired extremists is farcical and deeply worrying. Ever seen a fracking protestor set off a bomb? The answer is no, and any attempt to include them is an insult to democratic values, which include the right to dissent.”

This week, the government faces a legal challenge in the high court over claims that parts of its programme go against the right to free speech. The action is being taken by a British Muslim activist who claims he was identified as a “non-violent extremist” as part of Prevent.

In April the UN’s special rapporteur on the right to freedom of assembly said attempts to identify and counter Islamist extremism through the Prevent programme had “created unease around what can be legitimately discussed in public”. Other high-profile critics have included David Anderson QC, the independent reviewer of terrorism legislation, and the Commons home affairs select committee, which called for Prevent to be abandoned in favour of a more inclusive “Engage” title.

The Prevent strategy has been described as a counterproductive “big brother” security operation by the UK’s Muslim communities.

Last Monday, a government report into social integration in Britain, which found that some communities had become increasingly segregated, also contained a significant section devoted to Prevent. Commissioned by David Cameron as prime minister and carried out by Dame Louise Casey, the review found that the programme had disrupted more than 150 attempted journeys to Syria or Iraq to join the conflict, including action by the family courts to protect approximately 50 children from being taken to the region last year.

Casey’s review also claimed that the agenda of Prevent’s critics was to alienate Muslims from mainstream society.

One passage stated: “In some cases, local leaders have been too ready to complain about Prevent without any real understanding of its work or knowledge of its community-based projects and partnership working with local people on the ground.

“More worrying are some elements of this lobby who appear to have an agenda to turn British Muslims against Britain.”

The Home Office said: “Prevent is about safeguarding people at risk of being drawn into terrorism – support for anti-fracking is not an indicator of vulnerability.”