The roads were empty when Linda Catt and her father drove their white Citroën Berlingo into London on a quiet Sunday morning. They could not have known they were being followed.

But at 7.23am on 31 July 2005, the van had passed beneath an automatic number plate recognition (ANPR) camera in east London, triggering an alert: "Of interest to Public Order Unit, Sussex police". Within seconds Catt, 50, and her 84-year-old father, John, were apprehended by police and searched under the Terrorism Act.

After filing a complaint, the pair, neither of whom have criminal records, discovered that four months earlier, a Sussex police officer had noticed their van "at three protest demonstrations" and decided, apparently on that basis, it should be tracked.

The two anti-war campaigners were not the only law-abiding protesters being monitored on the roads. Officers have been told they can place "markers" against the vehicles of anyone who attends demonstrations using the national ANPR data centre in Hendon, north London, which stores information on car journeys for up to five years.

Senior officers have been instructed to "fully and strategically exploit" the database, which allows police to mark vehicles with potentially useful inform-ation such as drink-driving convictions.

The use of the ANPR database to flag-up vehicles belonging to protesters has resulted in peaceful campaigners being repeatedly stopped and searched.

Documents released under the Freedom of Information Act reveal Kent and Essex police deployed mobile ANPR "interceptor teams" on roads surrounding the protest against the Kingsnorth power station, in Kent, last year.

The files reveal the pressure police placed on the local Medway council to assist with the installation of cameras on lamp-posts. Sergeant Keith Waymont, Kent police's ANPR manager, wrote to the council three months before the demonstration to complain its officials were not co-operating. He wrote: "When I put this to my bosses, they were less than impressed, given the importance of this operation as the new power station build is likely to create a considerable number of jobs for Medway."

But council officials had reasons to object. Internal emails reveal they were concerned temporary cameras could "alienate the community". One wrote: "I agree – under what powers are they looking to do that? Everyone has a right to drive down a road unless we are returning to the miners dispute tactics of the 1980s."

Police eventually succeeded in mobilising the Kent ANPR system, which appears to have been used to monitor protesters since four years ago.

The marker was placed on Catt's van on 10 March 2005 by a PC Sayer, of Sussex police, who had noticed it at anti-war protests. Sussex police told Catt the marker was placed because her van was "associated" with protests which had given rise to "crime, disorder and the deployment of significant resources". After she submitted a complaint, senior officers found their officer's actions had been "proportionate and appropriate", a finding upheld on appeal to the Independent Police Complaints Commission, which concluded that while her case highlighted the concerns over "the civil liberties or protesters", police had been acting in accordance with "national policy".

Catt has since discovered from Greater Manchester police that footage of her protesting at last year's Labour party conference, which she drove to in her van, is being stored on the National Public Order Intelligence Unit database.

Another protester, an IT manager who only wants to be known as John for fear of police retribution, said he was stopped more than 25 times in two and half years after a "protester" marker was placed against his Mercedes SUV. He said police were giving him inconsistent explanations for the stops.

"I heard every excuse under the sun: 'We've heard reports of suspicious vehicles in the area' or 'We're keeping an eye on high value vehicles moving through the area,'" he said. "One or two officers would be a bit more honest and say: 'Your number plate has flagged up on our system, we don't know why.' This was happening all over the country."

He finally decided to complain after a police armed response unit stopped him onduring an evening out with his wife in March 2008.

Documents revealed a marker "requiring stop checks" had been placed on his car by Lancashire police in 2006 after he attended a protest, described by the local paper as "peaceful", against duck and pheasant shoot near Preston.

Lancashire police said the marker had been placed "for a policing purpose" and due to "concerns about the nature of your involvement" in the protest".