“Our colleagues will come together this week to conclude this work,” Erdogan told a news conference with Russian President Vladimir Putin in Ankara.
The S-400 is Russia’s most advanced long-range anti-aircraft missile system and can carry three types of missiles capable of destroying targets including ballistic and cruise missiles.
The system can track and engage up to 300 targets at a time and has an altitude ceiling of 27 kilometers (17 miles).
On trade, Erdogan said cooperation between Ankara and Moscow was getting stronger “day by day”.
“Our bilateral trade volume with Russia increased 30 percent as of the first 10 months of 2017,” he said.
“We have a harmonious working environment at the political level.”
The two leaders have met eight times this year. Erdogan said Ankara and Moscow would hold a seventh High-Level Cooperation Council meeting in 2018.
Putin, meanwhile, said obstacles to trade and economic ties had been removed.
“Within the first eight months [of 2017] Turkish agricultural exports to Russia increased by 1.8 percent,” he said.
Moscow imposed sanctions on Turkey following the shooting down of a Russian jet over the Turkey-Syria border in November 2015.
Turning to the Middle East, Erdogan said Russia and Turkey were in agreement on the issue of Jerusalem.
“We have seen the same approaches with Putin,” he said. “We agreed to continue our contacts in this regard.”
The Turkish president added that Israel saw the U.S. recognition of Jerusalem as its capital as a chance to increase oppression and violence against the Palestinians.
“It is not possible for someone who possesses conscience, morals, principles, values to ignore these murders,” he said.
The shift in U.S. policy sparked demonstrations across the Muslim world and Putin said the U.S. decision destabilized the Israel-Palestine dispute rather than contributed to its settlement.
“The status of Jerusalem should be addressed through direct contacts between Israel and Palestine,” he said.
Erdogan has called an emergency meeting of the Organization of the Islamic Cooperation for Wednesday and Putin said Russia would attend as an observer.
The leaders also discussed Syria. Russia, Turkey and Iran are the guarantor states that brokered a cease-fire in Syria in December 2016, leading to the Astana peace talks.
Erdogan said the three nations would soon hold a repeat of talks held in the Russian resort of Sochi last month.
The trio had consulted on a political process in Syria, Erdogan said.
“As the guarantors of Astana, we will make a significant contribution to the process carried out in Geneva to find a permanent political solution to the Syrian conflict,” he added, referring to the UN-backed peace talks.
Putin, who earlier confirmed the Russian military withdrawal from Syria had begun, said “almost” all of Syria’s territory had been cleaned of terrorists.
“I would like to appreciate Erdogan's personal efforts and contributions to the solution works for Syria,” he added.
Another important topic was energy and Erdogan described energy ties as being at a “new stage with the TurkStream and Akkuyu Projects”.
The TurkStream pipeline will carry Russian gas to Turkey and Europe while Russia’s Rosatom is planning to start building Akkuyu, Turkey's first nuclear power plant, on the Mediterranean coast next year.
Erdogan said both Ankara and Moscow were “willing and resolute” to realize the projects “as soon as possible”.
Putin said TurkStream would increase Turkey’s energy security as well as expanding Russian gas routes.