In a speech given at the National Risk Shield meeting in Istanbul, the Turkish leader said the buildings will be "immediately destroyed".
He also added that once rubble removal operations are completed, the final number of new residential buildings and rural homes in zones hit by the earthquake will be concluded, according to Anadolu agency.
So far, a total of 608,000 independent sections in 214,000 buildings have been confirmed to have been severely damaged by the 7.8 magnitude earthquake that killed at least 50,000 people in Turkey and neighbouring Syria.
The earthquake was followed by a number of aftershocks, and left millions in both countries homeless. The Turkish provinces affected include Hatay, Diyarbakir and Adiyaman, while in Syria the governorates of Latakia, Idlib and Aleppo were badly hit.
Erdogan further stressed that the government will take into account several factors relating to ground and geological conditions during the construction process in the earthquake-hit zones.
He added that new buildings will not be higher than three or four stories above the ground, and reaffirmed that the reconstruction projects will be more "secure and resistant" to potential disasters.
In the aftermath of the earthquake, around 160 building contractors were formally arrested for violating safety standards and for being involved in the construction of buildings that had collapsed following the disaster.
Suleyman Soylu, the Turkish interior minister, said that at least 564 suspects were identified.
Construction codes that meet engineering standards are rarely enforced in Turkey.
Experts say inadequate construction standards increased the earthquake's devastation, as well as Erdogan’s seemingly "slow" response to the disaster, to which he admitted.
The president, who was already under scrutiny for Turkey’s economic woes and the plunging of the lira, was criticised by survivors for not providing sufficient rescue and aid workers during the first few days of the devastating earthquake.
Erdogan, who will be seeking to extend his term as president in the country’s upcoming elections, vowed to complete rebuilding houses within one year.