Spit hoods, which are designed to prevent people spitting at police officers when they have been taken into custody, were used on at least 68 children in England in the first nine months of 2017, figures obtained by Crae through a Freedom of Information request show.
The 2017 figure - which includes one instance of a spit hood being used on a 10-year-old boy - is more than double the 2016 tally of 27 children and five times more than the 2015 total of 12.
Earlier this year, Crae raised concerns about the use of spit hoods, claiming that their use on children is potentially life threatening. The practice is used by 20 out of the 40 police forces in England.
The new figures are included in a Crae's State of Children's Rights 2017 report, which also includes traumatic and distressing reports from children who have been subjected to a spit hood.
The report also highlights concerns over the use of Tasers, stop-and-searches and police cell detentions on children under 18.
It said police leaders had become more proactive in developing policy and guidance to improve the treatment of children by the police, "however, significant improvements in practice and frontline policing are needed if children's rights are to be respected", it said.
According to the study, despite a drop of more than 50 per cent in the number of under-18s being arrested in the last six years, controversial practices such as hooding and the use of Tasers had risen significantly.
There were at least 519 uses of Tasers in 2016, an increase of 25 per cent from 2013 and last year Tasers were discharged or fired in 42 of these uses - the youngest child to be fired on was 12 years old.
The charity said it wanted the use of Tasers on children to be eliminated and the use of harmful devices on children by the police, including spit hoods, to be banned.
The study also revealed a 60 per cent increase in the number of families with children living in temporary homeless accommodation since 2010, of which many residences were not subjected to stringent and regular safety checks.
In terms of supporting young people with mental health issues, figures released by Crae showed nearly 60 per cent more children were admitted to specialist child and adolescent mental health (CAMHS) units in hospitals outside of their local area than the same period last year.
It also found more than a quarter referred to specialist mental health services were not accepted for treatment as they did not meet the eligibility criteria for specialist CAMHS.
Another key factor affecting children's health, development and wellbeing was the use of temporary accommodation.
The study found the numbers of homeless families continued to increase with the majority of these families placed in temporary accommodation, the use of which had also risen with 60,550 placements in 2017 compared with 37,940 in 2010.
"The right to thrive and have a decent standard of living is still under threat for many children, as cuts to social security are starting to bite with a disproportionate and detrimental impact on already disadvantaged families," the report said.
The charity, which compiled the research using evidence from experts and professional bodies, is calling on the government to ensure its ministers have a legal obligation to consider how its decisions will affect children and families.
Louise King, Crae's director, said: "Little or no attention is being paid to some of the huge dangers experienced by struggling families and ill-protected children who are being failed by our public institutions."