A total of 117 deputies in the 153-seat parliament backed the bill on fighting discrimination on racial, ethnic, political, religious, gender, sexual or any other grounds.
The law is aimed at bringing Croatia's legislation into line with the standards of the European Union, which the Adriatic country hopes to join by 2010.
The Catholic Church had demanded the exclusion in the legislation of the fight against discrimination based on "sexual identity, expression and orientation."
Croatia's main religious communities, including Islamic and Orthodox Christian, backed the Catholic stance and asked for the law to be "significantly amended."
"Under its current provisions, it is not possible to foresee the consequences the law could have in practice since it forbids discrimination in a broad way," the religious communities said in a joint statement.
The law could "jeopardise values on which Croatian society is based, among which figure notably marriage and family."
The Catholic Church fears the law could pave the way for homosexual couples getting married and adopting children.
"Besides taking care of the rights of minorities, the lawmakers should also represent the will, rights and values of the majority in our society, who are believers of all religions forming more than 95 percent" of the population, the statement added.
Non-governmental organisations praised the government for not caving in to pressure from the Church, which has considerable influence in many segments of Croatian society.
Almost 90 percent of Croatia's population of 4.4 million are Roman Catholics.
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