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But that situation could soon be coming to an end, with the Greek government having submitted legislation this week that would make compliance with Shariah optional in the wake of a clash between Muslim rules and Greek laws. Government officials said it would become law before an international court rules that the current arrangement breaches Europe’s human-rights standards.

Meanwhile, Turkish President  Recep Tayyip Erdogan is set on Friday to visit Thrace, where about a third of the 350,000 residents are Muslims who mostly speak Turkish. In a tense exchange with Greece’s president in Athens on Thursday, Mr. Erdogan said the rights of the region’s Turkish minority to uphold their traditions weren’t being properly honored.

His visit and his comments on the sensitive issue come on the heels of Wednesday’s debate in the European Court of Human Rights in Strasbourg, France, on whether to condemn Greece—where about 2% of the population is Muslim—for applying Shariah rules to family law.

The special status for Shariah law in Greece stretches back to the 19th century, when the country regained its independence after more than four centuries under Ottoman rule. Under an agreement set forth in the 1923 Lausanne Treaty, which said Thrace’s Muslim minority should be allowed to live under its customs, Greek legislation enshrined Shariah rules to govern family law for Muslims there.

Today, three muftis appointed by Greek authorities act as judges and enforce Shariah. That arrangement has persisted even after Turkey abolished Shariah in 1924 as part of Mustafa Kemal Atatürk’s push to modernize Turkey.

It was the case of Chatitze Molla Sali, a 67-year-old widow in Thrace, that upended the decadeslong balancing act between Greece civil laws and Shariah in the region.

Under that arrangement, marriage, divorce, alimony and child custody are organized under the rules set by the Shariah. Islamic law doesn’t recognize wills, however, instead applying set rules for what portions of an estate children and spouses receive. Sons, who are charged under Shariah with caring for a family’s women, inherit the majority of an estate.

“Wills bring hatred and discord in the families,” said Mustafa Imamoglu,  secretary to the mufti who adjudicates disputes under Shariah law in Komotini. “It would be like giving a dead person the opportunity to intervene in the lives of those still alive.”

When her husband died in 2008, Mrs. Sali inherited his entire estate under the terms of a will he had drawn up before a Greek notary. But the deceased’s two sisters disputed it, saying their brother’s Muslim faith rendered the will invalid and meant Shariah law should apply. Because the couple had no children, only a small portion of the inheritance stood to go to the wife under Shariah.

Greek courts initially dismissed the sisters’ claims, but Greece’s Supreme Court ruled twice that the inheritance must be settled under Shariah law. The case has gone to the Strasbourg court, which is widely expected to rule next year that Greece breached human-rights standards by allowing Shariah law to supersede civil law.

Government officials and locals say most Muslims in Thrace have viewed Shariah law largely as a way to maintain traditions such as the marriage ritual. But following the Greek Supreme Court decision, “what was given to the Muslims as a choice is now considered their obligation,” said Halil Mustafa, a local lawyer. “Most people don’t realize there is a problem with the current situation until it affects them.”

Indeed, as soon as Greece’s Supreme Court ruled the application of Shariah as compulsory, a number of local Muslims presented legal challenges to wills that had been considered settled. In one case, a man successfully challenged his father’s will that left all his belongings to his wife.

Other problems emerge occasionally in divorces, alimonies and child custody battles. Under Shariah, mothers have custody of girls until the age of 10 and boys until 8, but after that, children must move in with their father. In one case in Greece, the mufti ruled against a woman who was seeking to regain custody of her child from her mother-in-law.

Shariah law is applied in a few other Western countries, but on a voluntary basis. In the U.K., Shariah courts exist outside the state legal system to provide arbitration on family matters among Muslims if all parties agree. And Shariah is recognized by German courts in certain cases if no party to a dispute is a German citizen and if the ruling doesn’t conflict with German legislation.

The arrangement in Greece goes much further. From the 1920s until the 1980s, muftis’ decisions weren’t even translated into Greek. In the 1990s, a law was passed requiring that Shariah laws be translated and vetted to ensure they comply with the Greek constitution. “But in reality this never happens,”  Konstantinos Tsitselikis, a specialist in Balkan studies at the University of Macedonia in Thessaloniki. “The Greek courts just records and rubber-stamps the decisions.”

Ms. Sali’s case has pushed the Greek government to table legislation earlier this week that makes Shariah applicable only if both parties decide to abide by the decision of a mufti. Otherwise, decisions by Greek courts prevail.

Mustafa Mustafa, a Muslim and local parliamentarian with the ruling left-wing Syriza Party, hopes the new bill will be the first step toward abolishing Shariah entirely. “The local community in its vast majority shows…this is what it wants,” he said.

Looming behind the legal question is the sensitive issue of Turkish influence in Greece. in addition to the official muftis, two unofficial ones—funded by Turkey and elected by the local communities—are also in place to offer rulings. If Shariah loses its official status in the future, the Greek state will stop appointing the muftis, possibly yielding its influence over a legal system that will likely continue to hold sway in the Turkish-minority community.

“It is important for us to maintain the Shariah system, since Greece has the prevailing religion, Christian Orthodox, in its constitution,” said Ibrahim Serif, Komotini’s elected mufti, whom the Greek state doesn’t recognize. “We can make changes to the system, but we are not prisoners here. We are Muslims with Turkish roots and we are free.”

Write to Nektaria Stamouli at nektaria.stamouli@wsj.com