More than a fifth of councils still have a Bible reading or a prayer at the start of meetings, a Mail on Sunday investigation has found.
Communities Secretary Eric Pickles has also reaffirmed the freedom for town hall officials to say formal prayers.
The newspaper’s Freedom of Information Act request found that 59 out of 271 councils, 22 per cent, have a prayer or reading in their meetings.
In 2011 a legal challenge from the National Secular Society was brought against Bideford Town Council for saying prayers in meetings.
Last year the High Court ruled that town halls had no legal basis to hold formal prayers, even though Bideford Town Council has been doing so since Elizabethan times.
But the Government fast-tracked new legislation, effectively overruling the decision.
Mr Pickles said regarding the Mail on Sunday findings: “We have given clear guidance that councils can pray and councillors who want to do so should ignore any flawed advice that says otherwise.”
But he warned: “It’s clear that some politically correct town hall officials are still trying to marginalise faith and impose an illiberal and intolerant secularism.”
Just 19 councils said they have stopped holding prayers following last year’s case.
Bideford Town Council was supported in their legal case by The Christian Institute’s Legal Defence Fund.