Executive director John Petitti says the situation is challenging and concerning.
RCMP say two parents came forward last July after finding inappropriate text messages from an adult man to their teenage son.
Earlier this week, Nathan Labatt, who is 24, was charged with sexual exploitation, invitation to sexual touching and possession of child pornography.
He is to make his first court appearance in Humboldt, Sask., on March 23.
Police say Labatt was an active volunteer with Scouts Canada and the Roman Catholic and Ukrainian Catholic churches.
Petitti said Scouts Canada performs background checks and puts youth volunteers through vigorous training and monitoring.
He said it's rare that people who want to harm youth get through.
"It's a thing that keeps us awake at night," he said. "It's something that every youth serving organization around the globe deals with."