Many churches give out holy communion wine and wafers to the faithful. In Woking, Surrey, congregations can also queue up to have their free parking permits validated. But this privilege of churchgoing, however, is about to be challenged.

The National Secular Society (NSS) is challenging Woking borough council in the courts, warning that the exemption amounts to direct discrimination against non-believers who must still pay to park in the town centre on Sunday mornings.

The issue has become increasingly contentious as more councils scrap free evening and Sunday parking in pursuit of additional streams of income. The charges were initially denounced as a "tax on worshippers", so a number of local authorities – including Wyre council in Lancashire and Canterbury city council – responded by setting up "worship parking permit" schemes.

Woking, which established its scheme in May 2012, is the authority that the NSS has chosen to target for a test case, exploring whether the preferential treatment amounts to a breach of the Equality Act 2010.

Their letter of claim, sent by lawyers Leigh Day, explains that the local Anglican Christ Church, evangelical Coign Church and Trinity Methodist Church have all been provided by the council with ticket validating machines. Woking United Reform Church gives out council-backed parking permits to churchgoers valid between 9.30am and 1pm on Sundays.

The action has been brought in the name of Keith Porteous Wood, executive director of the NSS, who drove to Woking on Sunday 14 April and paid £3 to park his car in the Heathside Crescent council car park. Wood does not hold any religious beliefs.

"He was afforded no opportunity to park his car there without charge," the letter states. Those attending local church services parked in the same car park for free. Wood's "less favourable treatment" was because of religion or belief, Leigh Day argues in its letter.

Wood said: "The equal treatment of all, regardless of belief or non-belief, is a key secular principle. We have launched this challenge to preferential treatment of worshippers because it is neither legitimate nor lawful for local government to favour the activity of any faith (or non-faith) group through tax-funded subsidies."

One local resident, Aidan Griffin, who supports the legal challenge, said: "As someone who doesn't attend church, I should not be treated any less favourably than anyone else parking their car in Woking town centre on a Sunday morning. As a taxpayer, I'm also concerned about the loss of revenue to the council arising from this policy."

The society is calling for the scheme to be abandoned or for parking to be made free for everyone. Local Liberal Democrats have also opposed the scheme.

Peter Bryant, Woking council's head of democratic and legal services, said: "The policy applies to all faiths, not just church-goers. The council considers that places of worship, and the faith communities that they serve, play an important role, both in society in general and Woking in particular.

"They encourage people to participate in society, thereby promoting social inclusion. In addition, considerable voluntary work is organised by faith communities, often for the benefit of the more disadvantaged members of our society … In furtherance of this aim, the council allows members of a faith community to park free of charge.

"The council took legal advice. Counsel advised that it amounted to indirect discrimination, but could be justified on the basis that it was a proportionate means of achieving a legitimate aim."

The cost of the scheme was estimated to be £41,000 in 2012.