At least one boy under the age of 16 was castrated to 'help' his homosexual feelings while in Catholic church care in the 1950s, the NRC reported on Saturday.
But there are indications at least 10 other boys were also castrated, the paper said.
The claims were not included in the Deetman report on sexual abuse within the Dutch Catholic church published at the end of last year.
The paper says the one confirmed case concerned a boy - Henk Heithuis - who reported being sexually abused by priests to the police in 1956.
After giving evidence, he was placed in a Catholic-run psychiatric institution where he was then castrated because of his 'homosexual behaviour'.
Evidence
The paper says Deetman committee was informed about the castrations in writing but did not include mention of them in its report because 'there were few leads for further research'.
The Deetman committee was set up by the church itself in 2010 after the sexual abuse scandal broke.
It reported in December having identified some 800 priests and monks who abused children in their care between 1945 and 1985.
In addition, church officials, bishops and lay people were aware of what was going on but failed to take action to protect children, the report said.
Politician
The NRC also said on Saturday the final Deetman report did not mention that a leading politician with the Catholic people's party KVP had tried to have prison sentences dropped against several priests accused of abusing children in 1958.
Vic Marijnen, who went on to become prime minister in 1963, was chairman of the children's home where Henk Heithuis and dozens of other children were abused until 1959.
MPs are now calling for a full parliamentary investigation into the abuse scandal because of concerns about the neutrality of the Deetman inquiry.
MPs are due to question Deetman at a hearing next week.