Syrian state media reported the grim discovery as troops loyal to Bashar al-Assad and his supporters continued work to clear the city after driving militants out.
The government-controlled Syrian Arab News Agency (Sana) said at least 40 corpses had so far been recovered from the site, with some beheaded and others showing signs of “brutal” torture.
The report linked the discovery to a massacre documented in May 2015, when Isis militants were reported to have slaughtered more than 400 mostly women and children in Palmyra just two days after capturing the city.
State employees, their families and those believed to be loyal to the regime were said to be among those targeted.
Isis committed numerous atrocities during its reign over Palmyra, when its world-famous ancient ruins became a favoured backdrop for gruesome propaganda videos showing the execution of prisoners.
The Roman Arch of Triumph and Temple of Baalshamin were among the archaeological sites destroyed by the group, which left the area littered with improvised explosive devices and mines.
Explosions were rocking the former tourist attraction today as operations to safely detonate the bombs continued.
A Syrian officer said more than 3,000 mines have so far been dismantled with the help of Russian specialists.
"They booby-trapped everything, trees, doors, animals," he added.
An Associated Press crew described the city as “completely deserted” on Friday, saying the remaining civilians who lived under Isis had fled the onslaught by the Syrian Army and militias backed by Russian air strikes.
They re-captured the city on Sunday after weeks of intensive fighting and aerial bombardment.
Activists reported that most families had either voluntarily fled the city or being forcibly evacuated by Isis to other strongholds including its de-facto capital of Raqqa.
Gareth Bayley, the UK Special Representative for Syria, said he was “deeply concerned” by reports of pro-Assad militias abusing civilians and carrying out widespread looting.
The recapture of Palmyra was a strategic coup for the Syrian President, through which he hopes to convince the West that his forces are a credible partner in combatting terror as it ramps up the fight against Isis.
Additional reporting by AP
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