By Jalil Hamid and Syed Azman

(Reuters) - Malaysia's best known Christian convert, Lina Joy, lost a six-year battle on Wednesday to have the word "Islam" removed from her identity card, after the country's highest court rejected the change.

The ruling threatens to further polarize Malaysian society between non-Muslims who feel that their constitutional right to religious freedom is being eroded, and Muslims who believe that civil courts have no right to meddle in Islamic affairs.

"You can't at whim and fancy convert from one religion to another," Federal Court Chief Justice Ahmad Fairuz Sheikh Abdul Halim said in delivering judgment in the case, which has stirred religious tensions in the mainly Muslim nation.

He said the civil court had no jurisdiction in the case and that it should be dealt with by the country's Islamic courts.

"The issue of apostasy is related to Islamic law, so it's under the sharia court. The civil court cannot intervene."

About 200 mostly young Muslims welcomed the ruling outside the domed courthouse with shouts of "Allah-o-Akbar" (God is great), but Christians and non-Muslim politicians were dismayed.

"I think it's a major blow," opposition politician Lim Kit Siang said. "It casts a large shadow on civil liberties and the constitutional rights of Malaysians."

Malaysia's Council of Churches was saddened.

"We still go by the possibility that the constitution allows any citizen of the country to exercise his or her right to choose a religion and practice it," council secretary Rev. Hermen Shastri said outside the court.

"I don't think this decision is going to stop an individual from exercising that right for whatever reason."

DISSENTING RULING

The three-judge appeal bench ruled 2-1 against Joy. The dissenting judge, the only non-Muslim on the bench, said the department responsible for issuing identity cards should have complied with Joy's request to remove "Islam" from her card.

He accused the National Registration Department of abusing its powers. "In my view, this is tantamount to unequal treatment under the law. She is entitled to an IC where the word Islam does not appear," dissenting judge Richard Malanjum said.

Malaysia's Muslim Youth Movement welcomed the ruling, which asserted the overriding jurisdiction of the Islamic or sharia courts in cases centering on a Muslim's faith.

"We hope that we have seen the last of such attempts," said the movement's president, Yusri Mohamad. "We invite anyone who feels that they are aggrieved or victimized within the current system to choose other, less confrontational and controversial attempts towards change and reform."

In practice, sharia courts do not allow Muslims to formally renounce Islam, preferring to send apostates to counseling and, ultimately, fining or jailing them if they do not desist.

They often end up in legal limbo, unable to register their new religious affiliations or legally marry non-Muslims. Many keep silent about their choice or emigrate.

Lina Joy, 43, was born Azlina Jailani and was brought up as a Muslim, but at the age of 26 decided to become a Christian. She wants to marry her Christian boyfriend, a cook, but she cannot do so while her identity card declares her to me Muslim.

In 1999, the registration department allowed her to change the name in her identity card to Lina Joy but the entry for her religion remained "Islam".

Malaysia, like neighboring Indonesia, practices a moderate brand of Islam, but Muslims account for only a bare majority of Malaysia's population and are very sensitive to any perceived threats to Islam's special status as the official religion.

Malaysia has been under Islamic influence since the 15th century, but big waves of Chinese and Indian immigrants over the last 150 years has dramatically changed its racial and religious make-up. Now, about 40 percent of Malaysians are non-Muslim.