The government-championed measure, passed by parliament last month in the face of bitter opposition, was published today in the Official Gazette following Erdogan's signature yesterday, which means it has now come into force.
The law allows "muftis" as well as state-appointed civil servants to perform and register marriages.
Muftis are clerics employed by Turkey's state religious affairs agency Diyanet with the task of taking care of worship across the country.
Turkey is an overwhelmingly Muslim nation but an official secular state under its constitution as set up by Mustafa Kemal Ataturk, the founder of the Turkish Republic, in 1923.
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Until now, the law has stipulated that even religiously observant couples must be married by a state registrar from the local municipality, not a cleric.
Critics also claim the new law will open the way for unregistered marriages, and will breach Turkey's civil code.
The government however says a marriage conducted by a mufti is a civil marriage, arguing that the bill is actually regulating secular life, not religious life.
"The seeds of such a discriminatory practice are being sown today," he said.
Tanrikulu expressed concern in particular that the change will exacerbate an already existing problem in the country with child marriage.
According to UN children's agency UNICEF Turkey has one of the highest rates of child marriage in Europe with a rate of 15 percent of women married by 18.
But the law has been a priority for the government and in October, Erdogan told the opposition that the law would pass "whether you like it or not."
Erdogan and the Islamic-rooted Justice and Development Party (AKP) has been repeatedly accused by critics of eroding the secular pillars of modern Turkey.
Erdogan's governments have notably eased restrictions on wearing the Islamic headscarf in education, politics, the police and most recently the army.
The government rejects the criticsm, arguing it allows freedom of worship for all Turkish citizens and the lifting of headscarf bans merely brought Turkey into line with the rules in many Western, non-majority Muslim, nations.
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