Shabana Mahmood has been told that her crackdown on refused asylum seekers, including the forcible removal of children from the UK, will cause “significant harm”, in an intervention by an independent watchdog.

Rachel de Souza, the children’s commissioner for England, said the home secretary’s plan under consultation to push families – including those with children receiving ongoing medical treatment – to leave the UK should not be implemented as proposed.

She argues that the proposed changes could be in breach of the Children Act 1989, which says children’s best interests should always be at the centre of decisions about their lives.

Mahmood’s proposals were set out in a Home Office consultation in March which sought views on cutting support for families with a refused asylum application, cutting support for adult care leavers with a refused asylum claim, and legislating the use of physical interventions on children during enforced removals.

De Souza said: “I have a statutory duty to protect and promote the rights of children – that includes all children who arrive in this country, no matter how they get here or what their asylum status is.

“As they are currently set out, all three of the proposals will put children at risk of harm.”

De Souza has written to Mahmood to ask how many children this policy may affect, where they live, and what support they might need. Her office estimates that as many as 27,000 children could be affected.

“Despite my requests, the Home Office cannot assure me of the scope of the impact their proposals would have on children and families. I am therefore writing formally to the secretary of state to ask how many children will be affected by the proposals,” de Souza said.

In a speech in March, Mahmood said that failure to get control of the asylum system would be catastrophic. She said: “When people see small boat arrivals, at their current scale, or they feel the pace and scale of migration today, they feel like we have lost control.

“A loss of control breeds fear and when fearful, people turn inwards. Their vision of this country narrows. Their patriotism turns into something smaller, something darker, an ethno-nationalism emerges. The idea of a greater Britain gives way to the lure of a littler England. And other voices – voices to the far right – take hold,” she said.

Campaigners have warned that Mahmood’s plans could pave the way for sick children to be deported even if they cannot be treated in their homeland.

Under the proposals, ongoing medical treatment or unavailability of care in a refused asylum seeker’s homeland would not be viewed as a “genuine obstacle” to deportation. This would mean families – including children – would lose accommodation and support as they wait to be removed.

They would only have access to support if they would otherwise be destitute or have accepted reasons for not leaving the UK. Mahmood has suggested family members could be offered up to £10,000 each – capped at four people – to leave if their asylum application is turned down.

De Souza’s submission said proposals that ongoing medical treatment should not be considered an obstacle to leaving were at odds with the best interests of children. She called for this to be reversed.

She also said the Home Office should not act upon proposals to permit immigration and detainee custody officers to use force against children.

At present, immigration and other officers are not allowed to use physical interventions on children.

The consultation proposes physical interventions where an accompanied child does not comply with a requirement to leave the UK. Possible interventions include the use of handcuffs, the consultation said.

De Souza believes any force used against a child should be an “absolute last resort”, to protect them or others from harm and done so with the “upmost gravity” by trained professionals.