Anne Longfield, said she feared the financial crisis at Northamptonshire County Council would have “catastrophic consequences” for some children.
Both Northamptonshire and East Sussex councils are planning major service cuts due to funding shortfalls.
Ms Longfield wants the government to protect children from any council cuts.
Earlier this week, Tory-run Northamptonshire County Council has outlined a “radical” £70m savings plan, which did not rule out cuts to children’s services.
On Friday, the Conservative-led East Sussex County Council also put forward proposals to strip back services to a legal minimum.
Ms Longfield said she was particularly worried that the situation in Northamptonshire meant it would not protect “services for the most vulnerable children, which could have catastrophic consequences”.
Ms Longfield said the scale of the problem in England was highlighted by work carried out with the Institute for Fiscal Studies which showed “half of all the spending on children’s services goes on the 70,000 children who are in care”.
The commissioner warned: “If you add in those who are on the child protection registers, that’s over 80%, leaving very, very little for any others.
“Councils have been warning for some time that they are not going to be able to meet their statutory requirements.
“I can see and hear every day from families and children who simply can’t get help.”
She continued: “If you don’t help children when the problems aren’t at crisis point then the crisis is going to be developing and also it is going to be much more costly when it gets to that point.”
Ms Longfield added that money in the system had remained the same for 10 years but was now being spent on “fewer children who are costing more”, with the Local Government Association warning of a £2bn “black hole”.
‘Spending will rise’
However, Tory MP Chris Philp, ministerial aide to Communities Secretary James Brokenshire, said councils were getting more money.
“We have had to save money as a country because we had an enormous deficit eight or nine years ago,” he said.
“But one of the areas that local councils across the country have quite rightly protected are children’s services.
“The National Audit Office reported in March that real terms spending on children’s services has gone up by about 3%.”
Over the next two financial years “the spending power that local authorities have in real terms is going to go up by about £2bn,” he added.>