The education secretary has written to council leaders in England to express "concern" over the use of unregulated accommodation to house under-16s.
Gavin Williamson said these placements for children in care should be "eliminated".
This type of accommodation is not registered to deliver care.
But in October, Newsnight found that more than 100 children under 16 in England and Wales were living in such places, on any given night.
Mr Williamson said he could not "imagine a circumstance under which a child under the age of 16 should be living in an independent or semi-independent setting".
Unregulated accommodation is often flats and houses with support workers on site or visiting, but can also be hostels and lodgings or even hotels and holiday parks.
Running an unregistered home that provides support but not care for children under 16 is not illegal.
But it is potentially a criminal offence to run a children's home that provides care without registering with the regulator Ofsted or the Welsh Care Inspectorate.
"I am concerned about the number of children under 16 placed in settings that are not registered with Ofsted, so should not be delivering care, and I am certain that you will want to pay immediate and close attention to those placements," Mr Williamson wrote to local authority chief executives.
"I look forward to working together to make sure these types of placements are eliminated," he added.
"Such settings must only be used for older children who are ready to live with the level of independence afforded by these settings."
Teenagers in semi-independent care are treated as young adults and expected to do things like open bank accounts, wash clothes and buy food.
'Amy', who lived in an unregulated home when she was 17, said the minister's concern was "completely right".
"It's just neglect to put under 16s in these places," she told Newsnight.
"They need to be finding better places to put kids. They're creating more problems for society in the future. "
'Emma', who was placed in an unregulated placement last year at the age of 15, also welcomed the intervention.
"It is not the right environment for someone so young," she said.
The mother of a boy, 15, placed in an unregulated home, told Newsnight she was horrified when she realised the placement was not registered with Ofsted.
"Ofsted is important to me because it is telling me that a place is fit for purpose and has been checked."
The placement was more than 100 miles from the family home.
"I was told it would be for twelve weeks only. But my son was there for nearly a year. He received no structured education for most of the time he was there and often stayed in bed until 4 pm."
Local authorities can pay to place children in unregulated accommodation if they deem it to be in a child's best interests, a place in registered accommodation cannot be found or a court approves the placement.
The BBC previously learned children as young as 11 years old are being placed in these homes.
A freedom of information request carried out by Newsnight revealed that at least 63 local authorities placed under-16s in unregulated accommodation in the past three years.
Chris Wild, who manages a home for teenagers aged 16 and above, said he has refused to take children under 16 because it was "unsafe".
"At 15 you might be in care with an 18-year-old, who's been arrested for something sinister, or is affiliated with county lines drugs," he told Newsnight.
Newsnight has been investigating this part of the care sector, as part of its Britain's Hidden Children's Homes series.
Previously, the programme revealed that, according to figures from the Department for Education, about 5,500 looked after children in England were living in unregulated accommodation, up 70% from 2,900 10 years ago.