"The delivery of parts belonging to the system will continue in the coming days", Turkey's defence industry directorate said separately. Trump said Turkey had not been treated fairly but did not rule out sanctions.
Esper said he planned to speak to his Turkish counterpart later in the day.
Turkey could face expulsion from the F-35 program and other US sanctions if it goes ahead with the S-400 delivery.
The first shipment of the Russian S-400 missile system has arrived in Turkey, according to the Turkish defence ministry, moving the North Atlantic Treaty Organisation member closer to a new standoff with the United States.
USA officials have previously threatened to cancel shipments of F-35 jets to Ankara and impose economic sanctions on Turkey through the 2017 Countering America's Adversaries Through Sanctions Act.
The United States has since threatened to impose sanctions against Turkey and cancel sales of US -made F-35 jets as federal officials have voiced concern over Russian Federation gaining access to its fighter aircraft technology.
Officials told Turkey if the S-400 purchase went through the country would be barred from the F-35 program.
Under possible USA sanctions, Turkey could face expulsion from the F-35 program, a move Erdogan has dismissed. "There's no problem and the process will continue in a healthy way going forward".
Sanctions would mark a new low in the already-tense relations between Turkey and the US. "Planting that air-defense system on Turkish soil could, by means of its powerful radar, help Moscow discover the secrets - and the vulnerabilities - of the F-35s that Turkey intends to acquire". The Turkish lira weakened against the US dollar before the ministry announced the arrival of the S-400 consignment to the Murted Air Base, northwest of Ankara.
Ankara and Washington are also involved in disputes over strategy in Syria east of the Euphrates River, where the United States is allied with Kurdish forces that Turkey views as foes. The Russian Ministry of Defense tweeted footage of the plane carrying the S-400s touching down in Turkey.
"Our talks on the Patriot issue are continuing", the state-run Anadolu Agency quoted Akar as saying.
The Obama White House "wouldn't let him buy the missile he wanted to buy, which was the Patriot", Trump told reporters during the G20 summit in Osaka, Japan last month. "It's a political statement that the United States doesn't have a hegemony and control over North Atlantic Treaty Organisation members and particularly over Turkey", Ashraf said. Turkey has said the offer does not meet its requirements, including possible future joint production.
Turkey, which was scheduled to receive its first aircraft later this year, has been among nine partner nations in the program. Earlier this month, U.S. Senator Lindsey Graham appeared to raise the bar for sanctions, saying they may be triggered only when the missile system is activated.
Washington has given Ankara until July 31 to cancel the S-400 purchase or have its pilots kicked off its F-35 training course and expelled from the US. In response, the Pentagon is expected to announce that Turkey will be barred from receiving the new F-35 fighter. Turkish media reports have said it could take until October for the system to be fully operational.