The church is for the tiny Syriac community in Turkey and will be built in the Istanbul suburb of Yesilkoy on the shores of the Sea of Marmara, which already has Greek Orthodox, Armenian and Catholic churches.
The announcement came after Prime Minister Ahmet Davutoglu met Turkey's religious leaders in Istanbul on Friday and said no faith that has lived in the country could be regarded as foreign.
"It is the first (new church) since the creation of the republic (in 1923)," a government source told AFP.
"Churches have been restored and reopened to the public, but no new church has been built until now," he added.
Turkey, which once had large Christian minorities, is now 99 percent Muslim and critics of the ruling Justice and Development Party (AKP) have accused it of trying to Islamicise its officially secular society.
However, as part of its bid to join the European Union, Ankara has made efforts to widen minority rights and return some seized property as well as restore churches, monasteries and synagogues.
Christians now make up less than 100,000 of Turkey's population of 76 million and are sometimes the target of attacks.
But the prime minister insisted that the ruling AK Party "does not discriminate between our citizens... the principle of equal citizenship continues to be our characteristic trait," he added.
He condemned recent attacks on mosques in Europe and urged the religious leaders he met with Friday to "speak up together against Islamophobia".
The country's ancient Syriac minority, which now numbers less than 20,000, live mostly in the southeast and tend to be either affiliated to the Orthodox or Catholic churches.
But their numbers have swollen in recent years by thousands of Syriac refugees first forced out of Iraq by war and sectarian violence and later by others fleeing the fighting in Syria.
During his visit to Turkey in November, Pope Francis denounced what he termed the current wave of "Christianophobia" in the Middle East, accusing Islamist radicals of "hunting" Christians.
The various Syriac churches are among the oldest surviving Christian denominations, and use Aramaic, the language of Jesus Christ, in their services.
The new Istanbul church will be built on land given by the local council and paid for by a Syriac group, the government spokesman said.