The UN Commission of Inquiry on Syria has warned the children are in a "particularly precarious" situation.
UN investigators on Thursday called for the children of IS fighters to be repatriated from Syria and said they could be harmed if the parents were stripped of their nationalities.
The UN Commission of Inquiry on Syria said in a report that the children were in a "particularly precarious" situation since they often lacked official papers.
"This, in turn, jeopardises their rights to a nationality, hinders family reunification processes and puts them at a higher risk of exploitation and abuse," the report said.
UNICEF last year estimated there were some 29,000 children of foreign fighters in Syria - 20,000 of them from Iraq - and most of them under 12.
Following the collapse of self-proclaimed caliphate of IS last year, foreign fighters from nearly 50 countries were detained in Syria and Iraq.
The UN commission called on governments to recognise papers issued by non-state actors such as the IS group and witness testimonies to allow the children to obtain recognised documents.
UNHCR human rights official Marie-Dominique Parent told the European Parliament in November that roughly 700 to 750 children with European links were being held in camps in northeast Syria, with 300 of them said to be French.
Some countries have started to repatriate the children - with or without their parents - on humanitarian grounds.
But the UN investigators criticised the practice of revoking citizenship of suspected IS fighters used by countries including Britain, Denmark and France.
Its report said the practice had "negatively impacted children, including their ability to exercise basic human rights".
"States have well-defined obligations to protect children, including from statelessness. Failing to abide by such fundamental principles would be a clear derogation of duty," Commissioner Hanny Megally said.
The report also criticised plans by some countries to repatriate children without their mothers, saying it could "run counter to the principle of the 'best interests of the child'".
The UN Commission of Inquiry on Syria was set up to investigate human rights abuses shortly after the outbreak of the Syrian conflict in 2011.