Europe is generally regarded as the most secularised continent in the world. But in few EU member states is there a complete separation between church and state. The old interweaving of religious and worldly authority still makes itself felt in many countries today.

In England, the head of state is also titular governor of the church and bishops are members of the House of Lords. Finland and Denmark still have an official state religion, and in Greece up until recently, the Orthodox church was in charge of the public civil status register. Everywhere, churches maintain a firm grasp on education, the care and medical sectors, and the media. Churches have formal and informal positions of exception by law, which are sometimes used to refuse public services such as abortion or same-sex marriage, or to evade secular authority in cases of child abuse.

Europeans may take a sceptical view of political leaders who are too quick to express religious faith in public (while in the US an atheist president is virtually inconceivable), yet churches have a greater influence on politics than many people realise. The Vatican has a special position due to the highly centralised organisation and its status as a state.

Worryingly, religion is also increasingly making its presence felt in the corridors of the European Union – even though the EU was designed as a strictly secular project. The treaty of Lisbon includes article 17 on the dialogue of the EU institutions with churches and non-confessional organisations. This forms the basis for an annual summit of religious leaders with the leaders of the EU institutions. Secular organisations are largely ignored.

José Manuel Barroso, the European Commission president, and Herman Van Rompuy, the European Council president, have special high-level cabinet officials whose job it is to maintain relations with churches. The EU has official diplomatic relations with the Vatican. The Conference of Catholic Bishops is one of the most powerful lobby groups in Brussels.

Other religions also have representatives in Brussels, but they are less influential than the Roman Catholic church. Their collective influence is not to be underestimated, however. In addition, religions have influence from the pulpit, if necessary by threatening excommunication if politicians adopt standpoints that are at odds with official doctrine.

We are witnessing the emergence of the European equivalent to the "religious right" in the US. Areas affected by this rise include women's rights, gay rights and sexual and reproductive health rights as well as healthcare (such as contraception, abortion, condoms and IVF). Freedom of expression is also affected, generally in the form of laws against blasphemy. Freedom of religion is often conceived as a collective right of religion to exempt itself from the law, particularly the EU fundamental rights.

Religious lobbies are, for example, highly active against the broad European anti-discrimination directive that is in the works. Under intense pressure from religious lobbies, the European commission was initially reluctant to table a directive by which discrimination against gay people could be combated.

Invoking religious freedom, the lobbies are negotiating exceptions to the ban on discrimination, including discrimination against gay people, or for the right of confessional schools to discriminate. In this way, discriminatory practices are effectively being written in stone, while the principle of equality is one of the explicit pillars of European unification.

The European commission scarcely dares to take action when member states invoke religious freedom to disregard EU-fundamental rights. For example, in the case of Lithuania, when a law was passed that bans the "promotion of homosexuality", effectively rendering gay people invisible.

The controversial Hungarian media law also includes a paragraph of this type, which states that the media must show respect for marriage and the institution of family, whereby the government aims to constitutionally enshrine the definition of marriage as being between a man and woman. The new Hungarian media supervisor has already qualified public expressions of homosexuality as in conflict with these standards, and therefore potentially punishable under the new law. Discrimination of this type is clearly in conflict with the ban on discrimination in the EU treaties.

In the asylum and immigration legislation, religious lobbies are advocating for a conservative definition of "family" for purposes of "family reunification", or against the recognition of homosexuality as grounds for seeking asylum.

The fight against HIV/Aids and the reduction of maternal mortality also form targets for the religious lobbies, which are attempting to impose their own sexual morals such as a ban on condoms.

This is abuse of freedom of religion, which was intended to protect the individual against oppression and coercion on the part of the regime. Religious organisations do not determine where the boundaries of fundamental rights should be set. The EU fundamental rights are currently in the process of finding increasing expression in legislation. It is unacceptable for this legislation to be biased according to a strict religious morality. It is high time for the secular nature of the European project to be re-emphasised. Europe doesn't do God.

Perhaps it is time to replace "freedom of religion" by freedom of beliefs or conscience, an individual right that can be claimed by 500 million Europeans in all of their diversity.