No other British children are expected to be repatriated from Syria in the foreseeable future, despite the announcement from the foreign secretary on Thursday that a small number of orphans who had been caught up in the conflict with Islamic State had been brought home.

Home Office officials view the repatriation of the children, who cannot be named for legal reasons, as highly exceptional – and there is unhappiness with the Foreign Office for potentially opening the door to more Islamic State returnees.

“We feel there are legitimate security concerns here,” a Home Office source said. “Returnees, even children, are a security risk – our view is that repatriations can only be looked at on a case by case basis.”

Boris Johnson said: “I think the situation in Syria is very difficult and very dangerous and I think it has been a great success that some orphaned children have been brought back.

“But I think it would be over-optimistic to say that we could do it in every single case – the military, logistical difficulties involved are very considerable but what I’ve said is that where the government can help then it should help.”

Both the home secretary, Priti Patel, and her predecessor, Sajid Javid, have taken a hard line over whether to allow the last of the men, women and children who lived under Isis to return home, after the collapse of its “caliphate” in March.

In some high-profile cases, such as Shamima Begum, who left Bethnal Green, east London, at 15 to live under Isis, ministers have stripped individuals of their British citizenship to prevent them from returning – although Begum has challenged that ruling in the courts.

The orphans’ repatriation has been pushed within government by the foreign secretary, Dominic Raab. In a short statement on Thursday night he refused to reiterate the Home Office line that potential returnees would be assessed on a “case by case basis” and instead said bringing back the children was “the right thing to do”.

No further repatriation cases are understood to be in the pipeline, despite calls from Save the Children for the UK government to bring back all British children in Syria, whose number it estimates to be about 60.

Orlaith Minogue, humanitarian advocacy adviser with the charity, called on ministers to rethink, given that “Syria’s bitter winter with its sub-zero temperatures is just around the corner”. She said that “innocents should not be caught in the crossfire” and that the government could find a way to repatriate all 60, arguing they “could recover to live full lives in the UK”.

Refugee children – there are more than 1,000 – are housed in large, insanitary camps, many of which are effectively in the control of the women also being held in them. They are some of the last people to have left Isis’s former Syrian territories as US air power and Kurdish-led ground forces closed in on them.

A court in Birmingham agreed to release some information about the children now safely back in the UK, but said their identity could not be disclosed to protect their welfare.

Judge Michael Keane, presiding, said: “It is plain that being orphans and being in a war zone they will have suffered emotionally and psychologically, the extent of which needs to be assessed and determined.”

The court heard that a family arrived in Syria in 2015 and that the children were orphaned during the civil war. The parents are understood to have been linked to Isis, although few other details can be made public.

On Thursday, Martin Longden, a British diplomat, met representatives of the Syrian Kurdish administration that still runs most of north-east Syria to agree the handover of the orphans, who were flown to London shortly afterwards and met by members of their extended family.

Keane said the children “had breakfast together with their relatives and they appeared to be in good spirits” and were driven to their family home.

“They have settled into the home and appear to be as happy as they could possibly could be in the difficult circumstances of their return,” he concluded.