Facebook has been accused of waging “intellectual persecution” against atheists and ex-Muslims, after it repeatedly allowed conservative Muslims to take advantage of the site’s inappropriate content flagging system to have pages run for Muslim apostates shut down.

On Monday two prominent pages, Ex-Muslims of North America, which has 24,000 followers, and Atheist Republic, which boasts 1.6 million followers, were shut down after being targeted by Muslim groups.

The two pages offer assistance to people who have left the Muslim faith. Both were deemed to have been “in violation of Facebook’s community standards.”

In response, president of Ex-Muslims of North America, Muhammad Syed, has written Facebook an open letter in which he accuses the social media giant of not doing enough to protect “groups vulnerable to malicious attacks”.

He wrote: “Ironically, the same social media which empowers religious minorities is susceptible to abuse by religious fundamentalists to enforce what are essentially the equivalent of online blasphemy laws.

“A simple English language search reveals hundreds of public groups and pages on Facebook explicitly dedicated to this purpose – giving their members easy-to-follow instructions on how to report public groups and infiltrate private ones.

With the help of the Arab Atheist Network, Mr Syed has identified a number of sites targeted in this manner. Atheist Republic has been shut down four times in the last two years, he said, but also attacked were A Science Enthusiast (750,000 members), Humanitarian Non-Religious (32,000 members), and the Arab Atheist Network (23,500 members), along with six others, all with followers numbering in the thousands.

“Arab atheists, Bangladeshi secularists, and numerous other groups have been under attack for years, as religious conservatives in the Muslim world learn to abuse Facebook’s reporting system to their advantage,” Mr Syed wrote.

The two pages at the centre of the row were reinstated upon appeal, but Mr Syed believes that Facebook should do more to protect them from malicious attacks. He has called for a “whitelist” of groups vulnerable to attack, and for Facebook users who regularly abuse the reporting function to be penalised.

Speaking to Heat Street he said: “Many of these groups are not simply pages – they are communities in which atheists who are abandoned by those around them find comfort, support and emergency assistance in case of persecution or abuse. The closure of these groups means the loss of these vital resources for the isolated and vulnerable.”