As many as 3,000 children born into Islamic State families are being housed in camps in north-east Syria, Unicef estimates, with many younger than six years old and living in “extremely dire conditions”.

The figure from the United Nations children’s fund is sharply higher than earlier assessments, driven in part by the arrival in al-Hawl camp of as many as 30,000 people from the last Isis enclave of Baghuz. The number of newcomers has overwhelmed camp officials, who are struggling to keep accurate records and provide food and shelter.

At least 1,000 more children born to at least one parent aligned to Isis are believed to be being held in Iraq. Many are housed with mothers who have been handed death sentences by Iraqi courts after summary trials in which little, if any, evidence is heard.

Isis releases video of fighters in Baghuz as Kurdish forces advance Read more

The fate of children in both countries has become a vexing issue for many nations whose citizens travelled to join Isis and now wish to return. There is some appetite for allowing children to return, but next to none for their mothers or fathers, many of whom face criminal charges and are deemed to pose a security risk.

Unicef’s regional director for the Middle East, Geert Cappelaere, said many of the children in Syria were unwanted in the camp, adding to their vulnerability. There has so far been little interest from third party countries to offer resettlement.

“We estimate that close to 3,000 children of foreign nationality are living in extremely dire conditions,” he said. “There are many more children of Syrian and Iraqi parents, unfortunately with the same Isis label, many of them younger than six years old. These are children, not terrorists. These are children entitled to a childhood, deserving a fair chance in life.

“We want special attention to be given to any children under the age of 18, girls and boys. They should never be separated from their families.”

Play Video 11:12 Isis has my kids: I won't stop till I get them home to the US – video

The plight of children born to foreigners who travelled to join Isis was underscored last week by the death of the newborn son of the British teenager Shamima Begum, who fled Britain four years ago as a 15-year-old. Begum’s citizenship was revoked after she gave interviews disavowing her ties to the UK, while at the same time asking to be allowed to return home.

Her three-week-old son Jarrah died last week after struggling to breathe for several days. The decision to cancel Begum’s passport was heavily criticised following the infant’s death and the UK has been urged to honour protection obligations for children. The Foreign Office saidit could not have mounted a rescue operation.

Cappelaere reiterated that countries whose citizens are in detention in Syria have primary responsibility for getting children to safety. They “need to take their responsibility to protect their children and to repatriate them, if this is in the child’s best interest.” he said. “Without that support, principled humanitarian action for children will remain an illusion.”

Ministers urged to help UK families of foreign fighters in Syria Read more

The International Committee of the Red Cross said on Wednesday that as many as 20,000 Iraqis could be transferred from al-Hawl camp to their homeland after an agreement was reached with Baghdad. Fabrizio Carboni, ICRC’s regional director for the Middle East, told Reuters the transfer could happen within “weeks or months”.

Many of the Iraqi families have been in al-Hawl since before the collapse of the last strip of land controlled by Isis, having fled Anbar province earlier in the regional unrest. Large numbers have been unwilling to return, fearing collective punishment at the hands of the Iraqi government, which has told the ICRC that returnees would face a security screening process.

“Obviously our approach is mainly a humanitarian approach,” said Carboni. “We don’t ignore the security threats or the political dimension of these returns.”

On the issue of children associated with Isis, he said: “We are aware it is a difficult issue especially in Europe, but we believe that on humanitarian grounds, even if you look at this through a security angle, the solution goes through a return of those children and mothers.”

Kurdish forces have claimed that all women and children have left Baghuzand are pressing ahead with a final assault. An Isis video released on Tuesday appeared to show numerous children in Baghuz, but it was unclear when and where it was filmed.