The US has for years urged nations to allow foreign fighters to return home and face prosecution for crimes committed under the ISIS flag, but many countries, including France, have declined to do so.
Other countries, like Britain, have stripped accused ISIS fighters of their citizenship, making them stateless.
Deputy US representative to the UN Richard Mills told the Security Council that repatriating ISIS foreign fighters is key to stemming radicalisation at camps where they and family members are being held.
“The continued presence of thousands of ISIS foreign fighters in detention centres and their associated family members and displacement camps in Syria and Iraq must be addressed,” Mr Mills said.
He said these camps were targets for ISIS attacks and radicalisation, and that the threat posed by the group and its affiliates remained “global and critical”.
The residents are mostly in Iraqi custody or in Kurdish detention camps in north-eastern Syria.
Al Hol in north-eastern Syria is home to more than 53,000 people. Thousands have suspected ISIS ties but many came to the camp to flee the extremists.
The bodies of the two Egyptian girls were found in the overcrowded camp's sewerage system days after they went missing, the Syrian Observatory for Human Rights reported.
The group said the girls had been beheaded, a form of killing frequently used by ISIS.
The US official noted that UN investigators can help in transparent prosecutions against ISIS members that will meet minimum fair trial guarantees and legal protection.
Mr Mills called for the government of Iraq to adopt legislation on international crimes, notably genocide, war crimes, and crimes against humanity.
“We have seen the terrorist group continue to use violence in Syria and Iraq and seek to refill its ranks by trying to break out captive ISIS fighters from detention centres and prisons," he said.
Several European countries have refused to repatriate adults, believing they should be tried in countries where they are accused of committing crimes.
Iraq’s representative at the UN, Muhammad Al Uloum, welcomed the fact that some member states mentioned how “important it is to repatriate some foreign fighters and their families and in front of this council.”
The UN tried to address the issue in 2018 by establishing the investigative agency with a mandate to collect criminal evidence and to identify and bring witnesses back to testify in home-country courts.
To date, the UN investigative team has provided evidence for 30 trials in 10 countries.
The head of the UN team, Christian Ritscher, said it has started collecting evidence of crimes committed against the Christian community in Mosul.
Mr Ritscher said it had identified leaders and prominent members of ISIS who took part in the attack and takeover of three mainly Christian towns in the Nineveh plains in July and August 2014.