The internet giant refused the charity's request to pay for an AdWords site-targeted ad because it contained "inappropriate content".
The Christian Institute said that Google explained in its refusal email that it had a policy that did not permit the advertisement of websites containing "abortion and religion-related content".
The institute wanted to pay Google so that every time the word "abortion" was typed into the search engine, its link would appear on the side of the screen. The draft ad read "UK abortion law -- news and views on abortion from the Christian Institute. ."
It has started legal proceedings against Google on the grounds that it is infringing the Equality Act 2006 by discriminating against Christian groups. It is seeking damages, costs and the permission to publish its ad.
A spokesperson for Google said: "We only allow ads that have factual information about abortion. We recognise that this is a very emotive subject and that people have strong views on both sides of the argument. Google takes no view on this issue one way or the other as a company."
The charity was seeking to promote its online articles on abortion ahead of the Human Fertilisation and Embryology Bill arriving in the House of Commons next month.
It claims that Google is happy to allow ads for non-religious sites with views on abortion and also allows ads for pornographic sites as long as the sex is consensual and does not involve children or animals.
Colin Hart, director of the Christian Institute, said: "Google promotes itself as a company committed to the ideals of free speech and the free exchange of ideas. It is against this standard that Google's anti-religious policy is so unjust.
"To describe abortion and religion-related content as 'unacceptable content', while at the same time advertising pornography, is ridiculous."