The decision could "provoke conflict," he said during a news conference following a meeting with Egyptian President Abdel Fatah al-Sissi.
Putin, who declared last week that he would run for a fourth term as president, has largely staked his legacy on Russia's revival as the dominant military power in its region and a counterweight to the West in the Middle East. His tour to shore up bilateral ties comes at a time when U.S. policy in the Middle East is in flux, amid Trump's decision on Jerusalem and apparent support for the rise of Crown Prince Mohammed bin Salman in Saudi Arabia, as well as growing questions about the future role and mission of the U.S. military in Syria.
The trip began with a surprise visit to Russia's Khmeimim air base in Syria, where Putin announced an imminent drawdown of Russian forces in the wake of his declaration of victory in Moscow's intervention in the Syrian war. Russian warplanes secretly flew to Syria in late 2015. It was Putin's first known visit to Syria.
At the air base, Putin ordered his defense minister, Sergei Shoigu, to begin the "withdrawal of Russian troop contingents" to their permanent bases.
But he left open the door to a continued Russian presence in Syria, saying that Russia's air base at Khmeimim and naval base at Tartus would keep operating. He promised further strikes "if terrorists raise their head again" — an apparent reference to forces in Syria's long civil war that sought to topple the regime of President Bashar al-Assad.
"We will deliver such strikes on them that they have not seen yet," he told military personnel at the air base in remarks carried by Russian news services.
Russia's military intervention in Syria bolstered Assad's government and gave Syrian forces a critical edge against rebel factions backed by the West and its Middle Eastern allies. Iran, another key supporter of Assad, provided military advisers and other aid.
U.S. defense officials cast doubt Monday on Putin's announcement of a troop withdrawal. Similar pronouncements in the past — including one in March 2016 and another in January — "don't often correspond with actual troop reductions," said Col. Rob Manning, a Defense Department spokesman.
The speech to the troops also had the whiff of a reelection campaign at times.
"You are victorious, and you are going home to your families, parents, wives, children and friends," Putin told pilots at the air base. "The fatherland is waiting for you, my friends. Have a safe trip home. I am grateful for your service."
The deployment of troops to Syria marked Moscow's first major overseas military campaign since the invasion of Afghanistan in late 1979 under the Soviet Union. In July, Russia extended its lease of the Khmeimim air base for 49 years, giving Moscow a military foothold in the region for generations.
Putin met at the air base with Assad, whose regime appeared close to defeat in the summer of 2015 before the Russian intervention. At the time, it appeared that Assad would be forced to step down.
"I have come, as I promised," Putin told him. While hailing the fall of the Islamic State, Putin also noted the rebuke to Western plans in the region. "Syria has been preserved as a sovereign independent state," he said.
Putin has been eager to declare the intervention a victory, and his March 2016 drawdown announcement came as Syrian troops backed by Russian air power and special forces made a final push to recapture the ancient Roman city of Palmyra.
Western leaders were skeptical that Russia would pull back its troops, and Russian forces later played a key role in the race by pro-government forces to retake territory ahead of the Islamic State's eventual collapse.
The intervention has showcased much of Russia's military might: new warplanes, helicopters and warships, as well as cruise missiles fired from the Caspian Sea. It has come at the cost of more than 40 Russian soldiers killed, according to official statistics. The deaths of a similar number of military contractors have been reported by Russian journalists.
In Cairo, Putin met with Sissi and discussed the conflicts in Syria and Libya, a possible resumption of direct air travel after a 2015 terrorist attack aboard a Russian charter jet, and Trump's decision on Jerusalem. The contract signed during a meeting between Putin and the Egyptian president calls for the construction and a supply of nuclear fuel for Egypt's Dabaa power plant, scheduled to begin operating in 2026. Russia has also signed agreements to build nuclear plants in Turkey and Jordan. Russia finished construction on Iran's Bushehr nuclear power station — a project begun by a German firm under the shah — and opened it in 2011.
Putin arrived in Ankara, Turkey, on Monday evening for talks with President Recep Tayyip Erdogan. The leaders discussed developments in Syria and elsewhere in the region as well as relations between their countries, Turkish officials said.
Alex Horton in Washington contributed to this report.