Mr Erdogan made the statement during a press conference with US President Donald Trump at the White House on Wednesday.
It comes after Mr Erdogan launched an operation last month to attack Kurdish fighters in the battle against Islamic State, due to the US pulling troops from the region.
The Turkish government claims the Kurdish fighters are terrorists themselves. The conflict has caused several thousand Syrians to be displaced. They have also been accused of targeting innocent civilians.
A reporter asked the Turkish president during the press briefing: "With what you're calling a realignment along the northern Syria border, a lot of Christians in that region are feeling very vulnerable. Groups on the ground are saying that attacks on Christians have increased under this new policy. And that they're not feeling safe any longer. Can you guarantee that the Turkish government will also protect Christians in that region? "
President Erdogan replied: "On the contrary, Keldani, Yazidi, and Christian minorities is an area where we're especially sensitive about, and we have certain, different plans — whether it be the ones remaining on the side of Syria — whose sanctuaries have been destroyed, whose churches had been destroyed — will see their sanctuaries getting revived and their churches will be reconstructed so that they can go back and start praying there again. And these are the plans that we're making for them."
The president added that Christian minorities living on Turkey's side of the border "have no problems whatsoever, but the ones remaining on the side of the Syrian territory will see their worshiping practices restored and revived in a special manner".
He said they are also getting healthcare and humanitarian aid.
In September, President Erdogan announced his plans to take a big part of the Syrian side of the border in order to allow millions of Syrian refugees currently in Turkey to resettle there. The area the president wants to take control of is where the majority of the Christian and Kurdish people live.
Mr Edrdogan's promise to protect Christians wasn't welcomed by some people who don't believe the president will stick to his vow.
Christian persecution charity In Defence of Christians said in a tweet that the president was lying.
"Turkish President Erdogan claims that he will work to protect Christians in the Middle East. Among the numerous Turkish crimes over the years, Erdogan's recent actions in Northeast Syria prove his words are nothing short of lies," the organisation said in the tweet.
Nadine Maenza, a commissioner on the U.S. Commission on International Religious Freedom also tweeted: "So hard to watch Kurds, Christians & Yazidis being attacked by Turkey in NE #Syria while President #Erdogan is in our country. They are guilty of war crimes against civilians. Time for sanctions and a no-fly zone."
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