Last year children waited an average of more than 56 weeks before a county court decided to take them into care or a supervision order was made. The family proceedings courts took an average of more than 44 weeks.
The total number of unresolved cases increased from 8,677 at the end of 2008 to 12,994 at the end of 2009.
Barnardo's said delays meant some children were forced to stay in abusive homes and called for a 30-week upper limit for proceedings.
Chief executive Martin Narey said: "An insecurity has spread through the family courts with additional, sequential expert assessments being routinely ordered.
"This paired with the evident lack of credence given to social workers, is causing unnecessary delay.
"The courts need urgently to reflect on the damage these delays are having on extremely vulnerable children.
"A year of a child's life is an inordinate amount of time for them to be trapped in desperate limbo, unclear of their future and very possibly at risk.
"During this time, these children might remain at home with neglectful or abusive birth families or be living in emergency foster care, expected to settle with families they may subsequently have to leave.
"At a time when stable relationships and secure attachments are vital for a child, they are instead engulfed in a period of uncertainty and confusion."
The figures, for England and Wales, were revealed in written answers to parliamentary questions from Liberal Democrat MP Annette Brooke.
Barnardo's said the data also revealed a "postcode lottery" for children awaiting care.
While county court proceedings in London in 2008-9 took an average of 65 weeks, the proceedings in Humber and South Yorkshire took just 46 weeks.
The figures only cover cases where a care or supervision order was made, not cases where such orders were refused, where emergency protection was given, or where children were put in secure accommodation.
Barnardo's said the Government should give "urgent consideration" to a number of measures.
These include ensuring that all cases are dealt with within 30 weeks, or 12 weeks for children under 18 months.
Hugh Thornbery, director of children's services at Action for Children, said: "Today's findings are a cause for serious concern.
"For children who are unable to stay with their birth families, entering the care system is an extremely uncertain and unsettling time, and it's critical that their care provision provides them with the stable and secure home environment that they need.
"Being left languishing in emergency foster placements for unknown extended periods of time can only have a detrimental effect on children, and risks giving them a false sense of security at a time when they need stability the most.
"More must be done to ensure that vulnerable and neglected children do not get left in this situation; only then will they be given the opportunities they deserve to achieve their life chances."
Last month a High Court judge slammed Manchester City Council for removing a severely disabled teenager from his foster home while abuse allegations against his carer were investigated.
The claims, relating to comments the teenager was said to have made at school about being locked in a wardrobe, proved unfounded.
Mr Justice Baker said the decision to remove the teenager from his home of many years was a breach of his human rights, the teenager's sister later branding the council "barbaric".
A Ministry of Justice spokesman said: "The government is committed to reducing unnecessary delay in care proceedings.
"A Family Justice Review is currently under way gathering evidence on problems in the current system and proposals for change.
"The panel leading the review shares Barnardo's concerns and has met their representatives to discuss suggestions for reform.
"4,000 extra sitting days were added to the family courts earlier in 2010 to deal with care cases and the Government will continue to monitor the situation.
"We are also exploring proposals to make better use of local performance groups to give local decision makers more ownership of the system, empowering them to tackle the local causes of delay.
"The government is clear that every child's case should be dealt with as quickly as possible to minimise trauma and keep young people safe from harm."
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