The US president said that the UK and other EU countries “should have taken back” the captured fighters and their families instead of leaving them in camps guarded by Kurdish forces.
Mr Trump has been widely criticised for abandoning the Kurds since he announced last week that American troops would be pulling out of the border area.
In an attempt to justify the US withdrawal, he claimed on Sunday it was “very smart not to be involved in the intense fighting”, even though his decision preceded – and effectively endorsed – Turkey’s military operation.
“The Kurds and Turkey have been fighting for many years,” he tweeted. “Others may want to come in and fight for one side or the other. Let them! We are monitoring the situation closely. Endless Wars!”
Syrian Kurdish officials on Sunday confirmed hundreds of detainees at the Ain Issa camp had escaped amid Turkish airstrikes and intense fighting in the area.
Mr Trump then tweeted that “Turkey and the Kurds must not let them escape”. He added: “Europe should have taken them back after numerous requests. They should do it now.”
Among the detainees at Ain Issa were British sisters Reema and Zara Iqbal, who married Isis fighters after travelling to Syria in 2013. The UK government decided to strip them of their citizenship rather than bring them back for trial.
Last week the US president, who has repeatedly criticised European countries for not taking back Isis families, appeared unconcerned by the possibility of a breakout.
“Well they’re going to be escaping to Europe, that’s where they want to go, they want to go back to their homes,” he said. ”But Europe didn’t want them from us. We could have given it to them, they could have trials, they could have done whatever they wanted.”
The US is believed to have taken custody of some of the most dangerous Isis prisoners, including the captured British “Beatles” suspects Alexanda Kotey, 35, and El Shafee Elsheikh, 30.
Other detainees at Ain Issa included Tooba Gondal, a former student from east London who is accused of recruiting teenage girls to join the terror group, and three English-speaking orphans who were discovered by the BBC shortly before the Turkish offensive.
Isis bride Shamima Begum, who has been told she will never be allowed back to the UK, is being held in a different camp, Roj, near the Iraqi border.
Mr Trump’s surprise announcement of a US withdrawal came after he spoke with Turkish president Recep Tayyip Erdogan over the phone.
Turkey claimed its military operation, launched on Wednesday, was designed to establish a 20-mile “safe zone” for refugees and described Kurdish forces as terrorists.
The Kurdish-led Syrian Democratic Forces has now struck a deal with Bashar al-Assad’s government to repel the Turkish offensive.
More than 130,000 people have been forced to flee border areas as a result of fighting between Turkish-led forces and Kurdish militia, according to the United Nations.