Malaysia has found itself once again in middle of a messy religious and judicial controversy after the country’s highest court earlier this week threw out a bid by a 28-year-old Indian woman who took her estranged husband to court in an effort to prevent him from converting the couple’s 2-year-old son to Islam.

The woman, a Hindu housewife and secretary identified only as R Subashini, went to the courts in an effort to prevent her 32-year-old businessman spouse, T Saravanan, who assumed the name Muhammad Shafi Saravan Abdullah and converted to Islam in 2006, from taking matrimonial proceedings to Malaysia’s syariah, or religious court. When Shafi converted to Islam and confronted Subashini with the news, she attempted suicide and was hospitalized. When she recovered, she discovered Shafi had converted their four-year-old son to Islam. She feared that he would not only convert the younger child, but that she would lose custody and visitation rights.

Subashini’s lawyers took the case to the civil system based on a July landmark ruling that stated that if one party was a non-Muslim, the syariah courts had no jurisdiction, a rare ruling in a series that has gone against civil jurisdictions and ignited concerns among non-Muslims that their rights are being trampled in favor of syariah law.

A three-judge panel of the federal court used a technicality to rule that Subashini’s request for an injunction was "premature and invalid" because according to Malaysia’s Law Reform Act, the wife can only file for divorce three months after the date of her husband’s conversion to Islam. Subashini’s divorce petition was filed nine days before the three months had lapsed.

In what observers say is a confusing decision, the court ruled that the divorce petition would continue to be governed by the civil courts. Marriages between Muslims and non-Muslims are forbidden by syariah courts in Malaysia and are thus ruled to be broken unless both parties convert. While such marriages are recognized in civil courts, the Islamic courts refuse to do so, and in several recent cases the civil courts have bowed to the syariah courts’ primacy.

Despite the ruling that the divorce petition would remain in the civil courts, Judge Nik Hashim Nik Abdul Raman, one of two members of the three-judge panel who ruled to dismiss the case, noted that the high court’s jurisdiction is limited, given the fact that Shafi is now a Muslim and thus governed by Islamic law rather than civil law. One judge dissented from the decision. “The civil and syariah courts cannot interfere with each other's jurisdiction," Nik Hashim said, an indication that the syriah court would probably eventually prevail and that Subashini would probably lose the fight over the child’s conversion.

Justice Sri Ram dissented to the ruling.

Malaysia’s civil libertarians wasted no time in criticizing the ruling. Aliran, the Penang-based reform organization, issued a statement saying that “R Subashini’s case is symptomatic of problems in the everyday reality of negotiating rights and legal jurisdictions under the Federal Constitution. We agree with Justice Sri Ram’s dissenting judgment on this case that the federal constitution ‘confers jurisdiction on a syariah high court in civil matters where all parties are Muslim.’ and that any other interpretation would be unjust towards non-Muslim spouses. The Federal Constitution is not simply a document. Certain interpretations on the matter of jurisdiction have far-reaching social consequences, beyond the two parties confronting each other in court.”

It is not the first difficult case the high court has adjudicated in favor of Muslims in what is rapidly becoming a society that is increasingly intolerant of the rights of religious minorities. Earlier this week, officials threatened to withdraw the publishing license of a Catholic newspaper because the paper used the word Allah in exchange for the word God. The authorities said the word Allah applied only to the Islamic version of god, something disputed by religious authorities, who pointed out that middle-eastern and Indonesian Christians often used the two words interchangeably, and that in fact the Islamic religion views itself as part of a religious continuum that began with Judaism and extended through Christianity. Jesus Christ is considered a Muslim prophet.

Also, in May, the high court ruled in a similarly split decision that a 43-year-old Kuala Lumpur woman who renamed herself Lina Joy had in effect lost a 12-year fight to change her designation on her identity card from Islam. She had become a Christian more than a decade earlier, forsaking her Muslim religion. However, the court ruled that the syariah courts had jurisdiction over whether Joy’s religious status would remain Muslim, which was tantamount to denying her claim.

Only once in history have Malaysia’s sayriah courts ruled to allow anyone to change religious identity and that case involved an 89-year old woman named Nyonya Tahir who converted to Buddhism in 1936. Her decision was accepted 69 years later in 2006, after she had died.