The decision has been welcomed by the teachers' unions, which feared that two of the provisions in the Bill could be used to discriminate against their members in denominational schools.
The Bill aims to protect employees from discrimination. If teachers feel they are discriminated against, they will be able to take a case to a director of equality investigations.
Religious institutions, however, are exempt in certain circumstances. They will, for example, be allowed to give more favourable treatment to co-religionists in terms of employment where this is necessary to protect the ethos of the institutions.
They will also be exempt if they take action to prevent employees from undermining the ethos of the institutions.
The churches had lobbied hard to retain the exemptions, arguing that they were necessary to protect the ethos of their schools.
The unions, however, countered by saying that the provisions could be used to discriminate against teachers whose lifestyles were not in accordance with the religious practices of the schools in which they worked.
At their recent annual conferences the unions pledged to support any teacher who was discriminated against in this way.
The secondary teachers' conference heard how several teachers had lost their jobs or been threatened with dismissal because of their lifestyle. The cases usually involved extra-marital relationships.
President Robinson is a constitutional expert and her decision came as something of a surprise to the government which believed it was on safe legal grounds in giving certain exemptions to the churches.
Some ministers were known to be unhappy at including the provisions but felt they had no other option.