An Anglican newspaper has defended the publication of an article that compares gay rights campaigners to Nazis, saying the author has "pertinent views".

The column, by former east London councillor Alan Craig, appeared in the 28 October edition of the Church of England Newspaper, one of the oldest newspapers in the world. Although it is independent of the institution bearing the same name, it carries adverts for Church of England jobs and is read by its clergy.

In his column Craig referred to a number of high-profile legal cases where Christians claim to have been penalised for their views on homosexuality.

He wrote: "Having forcibly – and understandably – rectified the Versailles-type injustices and humiliations foisted on the homosexual community, the UK's victorious Gaystapo are now on a roll. Their gay-rights stormtroopers take no prisoners as they annex our wider culture, and hotel owners, registrars, magistrates, doctors, counsellors, and foster parents … find themselves crushed under the pink jackboot.

"Thanks especially to the green light from a permissive New Labour government, the gay Wehrmacht is on its long march through the institutions and has already occupied the Sudetenland social uplands of the Home Office, the educational establishment, the politically-correct police. Following a plethora of equalities legislation, homosexuals are now protected and privileged by sexual orientation regulations and have achieved legal equality by way of civil partnerships. But it's only 1938 and Nazi expansionist ambitions are far from sated."

Craig told the Guardian he was "pretty careful" to distinguish between the leadership of gay rights groups and "ordinary gay people".

"I've nothing against ordinary gay people but the leadership, well I stick by my word Gaystapo. It is bullying. I oppose bullying and hatred in all its forms. There is no justification for the bullying or intimidation of gays and that has been rectified in law, but we've moved on to a new game. We're now seeing these attitudes of intolerance they accuse their opponents of."

The weekly paper, which was founded in 1828 and has a circulation of around 8,000, takes pride in its reputation of being a "bastion of conservative evangelicalism". Its editor, Colin Blakely, defended the "Gaystapo" article.

"He has got views that are pertinent on this issue. I was on holiday that week and if I had seen it I would have asked him to tone the language down somewhat. We're getting a lot of correspondence on this column. He has not won a lot of support with readers and we're publishing letters. We want people to engage with the issue."

Ben Summerskill, the Stonewall chief executive, condemned the column and the newspaper. "Given the horrific circumstances of the Holocaust, it is deeply disturbing and highly offensive that the Church of England Newspaper has chosen to compare supporters of equality with Nazis. We are sure that many of the paper's advertisers, such as the University of Sheffield, will be deeply disturbed to read this crass and homophobic article."

There is an increased perception among some Christian groups that it is harder for the devout to live out their faith because of legislation such as the Equality Act. Christian guesthouse owners Peter and Hazelmary Bull are in court this week trying to overturn a ruling that they broke the law by refusing to allow a gay couple to stay in a double room, while a group of politicians and peers are holding "select committee style" hearings to establish whether or not British laws discriminate against Christians.