Home Office transfers of unaccompanied minors who were registered in the Calais refugee camp have stopped, meaning up to 1,000 children are unlikely to be given sanctuary in the UK.

The immigration minister Robert Goodwill said more than 750 refugee children from Calais had arrived in the UK. Officials said all the children taken from the camp in early November had been interviewed and those eligible to enter the UK had been moved.

“Many have been reunited with family members already in the UK, while others are being cared for by local authorities across the UK. The remaining children are safe and in the care of the French authorities,” Goodwill said.

Charities expressed concern about the fate of those who had been interviewed and found to be ineligible for transfer. They said that if the Home Office closed the door to legal transfers, more unofficial camps would spring up near the port as children desperate to join relatives in the UK tried to make their way illegally via people traffickers and lorries.

Safe Passage, a charity that offers legal support to refugee children applying to join relatives in the UK, said it estimated several hundred Calais children remained in France despite having a legal right to be in the UK. It has more than 40 live cases of children it is trying to help to relocate.

Alf Dubs, the Labour peer whose amendment to the Immigration Act commits the government to giving homes to vulnerable refugee children travelling alone, said: “I’m dismayed to learn that transfers are about to cease having only just begun. Had the bridge been pulled up so soon after the start of the Kindertransport, through which my life was saved, many of us would never have made it to Britain.”

Mike Penrose, Unicef UK’s executive director, said: “Bringing 750 children to safety in the UK over the last six weeks is a real achievement. That progress is worth celebrating, but we must be clear that the job is not finished. The government must provide assurances that the system will continue to work for the children who have not yet reached safety. If sustained, safe and legal routes to the UK are not made available to children, they will continue to fall into the hands of smugglers and traffickers.”

Many unaccompanied minors currently dispersed around France complain that they have been left in the dark about their future by French and British authorities.

This week a Sudanese radiographer living in Liverpool after fleeing Darfur made an emotional plea to the government to be reunited with his teenage brother, who remains in France five weeks after the Calais migrant camp was demolished.

Mohamed Adam Hamad Ahamed said he was becoming increasingly anxious about the mental state of his 17-year-old sibling Moubrak. He had fled death threats in a Darfur camp for displaced people and now faced another “situation” in France, he said.

His hopes of seeing his brother for the first time in two years were raised when he received a phone call from a Home Office official in mid-October. But he has not heard anything since.

Although the remaining children from Calais look unlikely to travel to the UK, the Home Office said it would continue to transfer other children from Europe in coming months. “The Dubs process has not ended. More eligible children will be transferred from Europe, in line with the terms of the Immigration Act, in the coming months,” Goodwill said.