The commission was set up in May 2010 after a similar investigation into Catholic boarding homes began also receiving complaints of abuse in non-Catholic institutions. The Catholic investigation found that around 10 percent of children who attended them may have been sexually abused, compared with around 7 percent nationally.
The problems at state-funded institutions appear to have been equally bad, if not worse, the commission's chairwoman, Rieke Samson, said on Monday.
"We can no longer ignore sexual abuse in child care," she said. She said short-term measures to fix the problems would be insufficient, and a "change of culture" was needed "from high to low, from minister and bureaucrats to guardians and group leaders."
She said that since 2010 her commission has received more than 800 complaints, some dating back decades, and has referred 42 recent cases to prosecutors.
The commission found that more than half of abuse came at the hands of other, often older children. Adult men were the abusers in around two-thirds of the remaining cases, while girls made up two-thirds of victims.
Perhaps most worrying, the commission estimated that only about 2 percent of abuse cases are ever detected by the current system.
"There are few quality requirements and there's actually too little capacity for independent" checks on the system, Samson said.
The cycle of commissions and investigations looks set to continue. Child Care Netherlands, which oversees child services, received the harshest criticism in the Samson report.
It apologized to victims and said Monday it is setting up a commission to investigate how sexual abuse can be prevented, or at least reduced.
"I wish that we could take the pain away, but we can't," said spokeswoman Ans van de Maat.