Hulusi Akar announced the move in an interview with the state-run Anadolu news agency on Saturday.
Ankara and Washington agreed to set up the joint facility earlier this month after difficult negotiations.
The centre will help coordinate the establishment of a buffer between the Turkish border and Syrian areas controlled by the US-backed Kurdish People’s Protection Units (YPG).
“The joint operation centre has started working at full capacity. The command of the centre is by one US general and one Turkish general,” Akar was quoted as saying.
He added that the first joint helicopter flight was due to take place on Saturday.
Turkey and the US have been at odds over plans for northeastern Syria, where the YPG formed the main part of the US-backed Syrian Democratic Forces (SDF) fighting the Islamic State of Iraq and the Levant (ISIL or ISIS) group.
Ankara considers the YPG a “terrorist” group aligned with the banned Kurdistan Workers Party (PKK) and has repeatedly threatened to launch a new military offensive to clear the Kurdish forces from along its border with Syria.
The joint operations centre was initially suggested by Washington to dissuade Turkey from carrying out another cross-border attack, after previous offensives in 2016 and 2018.
Syrian President Bashar al-Assad‘s government has called the safe zone agreement a serious escalation that violates its sovereignty. It said it was part of Ankara’s “expansionist ambitions” in Syria.
Al Jazeera’s Bernard Smith, reporting from Antakya in Turkey, said details of the safe zone were unclear.
“What is missing from Akar’s comments is what exactly the safe zone is, how big is it and who patrols it,” he said.
In addition to pushing Kurdish forces away from its borders, Turkey was pressing for a safe zone because of the ongoing Syrian government offensive to take control of the northwestern province of Idlib and surrounding areas, said Smith.
The region is the last rebel stronghold in Syria.
“Syrians escaping the violence are heading north towards the Turkey border, half a million are heading that way according to the UN. Turkey is not going to let them in, it doesn’t want them gathering along the border so it wants the safe zone established,” he said.
Meanwhile, the SDF said they would help implement the buffer zone in their areas along the Turkish border.
General Mazloum Abdi, commander in chief of the SDF, said his group will do all it can to ensure that the understandings between the US and Turkey are successful.
The SDF will be “a positive side in bringing” stability to the whole region, he said in a speech in the northeastern province of Hassakeh.
“We will exert all efforts to achieve accord with the Turkish state in coordination with the United States,” he added.