The details emerged from an unprecedented public investigation by Spain’s ombudsman, who spoke of the “devastating impact” on victims.
Angel Gabilondo also criticised the Church for its inaction and attempts to cover up or deny the abuse.
“What has happened has been possible because of that silence,” he said.
The 700-page report, which was ordered by Spain’s Congress last year, reveals the result of a survey that the commission carried out on 800,000 members of the public.
It found that 0.6% of the country’s adult population, roughly 39 million people, said that they had suffered sexual abuse as children by members of the clergy.
That percentage rose to 1.13%, more than 400,000 people, when including alleged abuse by lay people in institutions overseen by the Church.
While Mr Gabilondo said on Friday that the Church did cooperate with the commission to a certain extent, he highlighted its lack of interest in assisting with the report and the hostility of bishops in some dioceses.