Malaysia’s highest court on Wednesday ruled that Islamic law took precedence in cases of apostasy in a case seen as a key test of religious freedom in the multi-ethnic country.

Lina Joy, a former computer saleswoman disowned by her Muslim family for converting to Christianity, had appealed to the federal court seeking government recognition of her conversion. Malaysia’s Islamic law courts, whose jurisdiction applies to more than half the country’s 27m population, consider conversions a crime.

The latest court ruling suggests that people born as Muslims in Malaysia do not have a choice of religion in spite of constitutional guarantees. It could thus strengthen fears among Malaysia’s ethnic Chinese and Indian minorities about what they believe is the increasing Islamisation of the country.

The federal court in a 2-1 decision concluded that secular courts could not interfere with decisions made by Islamic shariah courts on issues of Muslim family law. The court’s lone non-Muslim judge dissented from the majority decision, saying Ms Joy should have the freedom to choose her religion.

The decision will strengthen the powers of the shariah courts. It could also limit the intervention of the secular courts in other family disputes involving Muslims and non-Muslims.

Ms Joy had been seeking to have the government remove the word “Islam” from the religion category on her state identity card without seeking shariah court approval. She argued that the jurisdiction of the Islamic court no longer applied to her once she converted to Christianity.

Muslim groups welcomed the decision as offering greater protection for Islam, which they say is under threat from liberal influences.

“It should be seen as a rejection of attempts by certain individuals, certain parties to deconstruct and revamp our current formula,” said Yusri Mohammad, the head of the Muslim Youth Movement.

The decision will affect several other pending high-profile cases, including ones involving the custody of children born to parents of different faiths.

“It’s a major blow and a grievous setback to Malaysia as a secular nation,” said Lim Kit Siang, leader of the Democratic Action party, the country’s biggest opposition group.

“It has cast shadows over fundamental liberties and civil rights in the country.”

Ms Joy, who has said she fears for her life due to publicity over the case, could now be subject to punishment for apostasy if the Islamic courts decide to pursue the case.

In Malaysia, the offence is punishable by fines and jail sentences, with some offenders sent to rehabilitation centres.