Russian-backed Syrian government troops on Thursday recaptured the historic city of Palmyra from Islamic State for the second time, the Syrian army said in a statement.

Islamic State fighters planted mines and explosives—a common tactic used by the extremist group as it is pushed back in its Syrian and Iraqi strongholds—as they fled the advance, according to the army and the U.K.-based Syrian Observatory for Human Rights, an opposition monitoring group. The troops were supported by Russian warplanes, they said.

The loss of Palmyra, a Unesco World Heritage site home to some of the region’s oldest and most venerated historic sites, is the latest military setback for Islamic State. It has lost a number of key battles since 2015 and is now fighting for control of Mosul, its remaining urban stronghold in Iraq. Turkish-backed rebels last month also captured the northern Syrian city of al-Bab from the group.

Islamic State had retaken Palmyra in December 2016, in what was seen as a resounding embarrassment for President Bashar al-Assad’s forces and their Russian ally, after having driven the militants from the city that March.

The regime’s second loss of Palmyra came in December as its forces, aided by foreign Shiite Muslim militias, had been slowly regaining control of the city of Aleppo after months of intense fighting.

Even bolstered by domestic militias and thousands of foreign fighters, it has struggled to maintain a force capable of battling opposition rebels and Islamic State on multiple fronts.

Thursday’s victory carries military and symbolic significance for the regime and key ally Moscow, both of whom have claimed to be fighting terrorism in Syria.

“The liberation of Palmyra is a powerful symbol of Syria’s liberation from the infection of terrorism,” Konstantin Kosachyov, head of the upper house of the Russian parliament’s committee on foreign affairs, told the country’s Interfax news agency.

Russia began backing Syrian forces in October 2015, with the stated goal of defeating terrorist groups in Syria. It has since been accused, including by Western officials, of using air power mainly to attack the more moderate rebel groups seeking to overthrow Mr. Assad.

Recapturing Palmyra “proves that the Syrian Arab Army in cooperation with [its] friends is the only effective force capable of countering and eradicating terrorism,” the Syrian army said in its statement.

Syria’s army “will continue to fight terrorism, specifically Daesh,” said Talal al-Barazi, the governor of Homs province, where Palmyra is located.

The seizure of the historic site caused global outrage and concern about the fate of the ruins, including many statues and temples which Islamic State militants believe are forbidden by their extreme interpretation of Islam.

Islamic State first seized Palmyra in May 2015.

Before the Syrian army’s first recapture of the city, the militants had blown up parts of its historic landscape and destroyed the more than 2,000-year-old Temple of Bel, one of the region’s most revered historic sites.

The destruction continued in their second hold on Palmyra. In January, they destroyed the Tetrapylon, a cubic-shaped ancient Roman monument, and parts of the revered Roman Theater, according to Palmyra Monitor, a group of independent activists based in Turkey.

Islamic State’s territorial foothold in Syria still includes large parts of the provinces of Raqqa—its de facto capital—and the oil-rich eastern province of Deir Ezzour, where it is besieging the Syrian army. Deir Ezzour abuts Iraq and is a bridge between Islamic State’s areas of control in the two countries.

The army and its allies will likely next move toward breaking the siege in Deir Ezzour, Mr. al-Barazi said, though he didn’t give a time frame.

—Thomas Grove in Moscow contributed to this article.