WCVB-TV reported Walpole police said staff at The Home for Little Wanders didn't immediately report an alleged rape to them. The organization runs the Longview Educational Center, a youth home in Walpole for children in DCF custody.
Authorities said a 13-year-old boy enrolled at the center raped a 9-year-old boy.
Walpole police said they learned of the incident 12 hours after it happened, making it "impossible" to collect evidence.
Michael Pearis, executive vice president of The Home for Little Wanderers, disputed the account provided by police.
"We are unable to provide further information at this time and ... felt it would be irresponsible for the media to refer to this incident as an alleged sexual assault or rape," Pearis said in a statement, according to WCVB-TV.
Last month, DCF Commissioner Olga Roche resigned after a pair of infant deaths. Authorities said DCF's lack of communication with police may have contributed to at least one of the deaths.