The Coalition's first foray into the defence of Christianity
The litigation comes after atheist councillor Clive Bone raised objections to the prayers being integrated into proceedings.
Holding prayers before council meetings is 'not appropriate in modern-day Britain' and may even be putting off potential members, the NSS believes.
They argue that formal recitation of prayers at the meetings breaches Article 9 of the European Convention of Human Rights, which protects freedom of thought, conscience and religion. Now the group is seeking a judicial review to settle the issue.
NSS executive director Keith Porteous-Wood said: "We've instructed our solicitor to go the High Court. We had a complaint from a Bideford councillor (Mr Bone) about the prayers. He's an atheist and found it embarassing and inappropriate that this should be an integral part of the meeting."
Writing on the NSS website, he explained: "The councillor objects to being subjected to prayers, or having to leave the chamber while they are said. Elected councillors of public bodies should not be put in such an uncomfortable and embarrassing position. The council's purpose is to provide local services, not church services.
"The councillor is aware of potential councillors who are put off becoming candidates because of this archaic practice. The practice is therefore interfering with operation of local democracy.
"There is a chronic shortage of candidates and unnecessary obstacles to new councillors should be discouraged.
"It is nonsense to claim that the rights of councillors to manifest their religion would be restricted if the review is successful.
"Councillors can, like anyone else, go to church or pray at home whenever they wish, and indeed we do not have a problem with them praying separately before or after council meetings.
"But it is not appropriate in modern-day Britain for prayers to form an integral part of the council meeting."
Letters written to the council, claiming that the prayers are illegal, have not changed its attitude, leaving the NSS to take legal action, he said.
A win in the High Court would set a precedent as thousands of other councils (not to mention both Houses of Parliament) also say prayers before their meetings. Similar issues with pre-meeting prayers have arisen at Wellington Council, Shropshire, Torbay Council, in Devon, and at Whaley Bridge, in Derbyshire.
Mayor of Bideford Phil Pester said: "We took the decision that we would see what the judge says about it. It won't cost us anything at this stage. If the judge decides it is illegal then, fair enough, we will think again. Until such time we are sitting tight. We took two democratic votes on this and there has been a substantial majority in favour of the prayers. We only have 12 full council meetings a year. The prayers last about four minutes. It is a minuscule amount of time."
But the new Communities Secretary Eric Pickles has responded rather robustly, saying: "While I cannot comment on a specific court case, the new Government recognises and respects the role that faith communities play in our society.
"Prayers are an important part of the religious and cultural fabric of the British nation.
"While the decision on whether to hold prayers is a matter for local councils, I want to ensure that they continue to have the freedom to do so."
Freedom to pray? Freedom to maintain the distinctive Christian character of the nation? Freedom to preach orthodox Christian views? This is The Coalition's first foray into the religion-equality quagmire created by Labour.
Eric Pickles, Defender of the Faith.