Josh Powell denied the accusation from the assistant attorney general for Child Protective Services, John Long, who spoke at a hearing to determine who will take custody of the couple's children.
Susan Cox Powell has been missing since 2009. Josh Powell has been the only named person of interest in the case.
Powell and his young boys have been living in Puyallup at the home of his father, Steven Powell.
Steven Powell was arrested last week and charged with voyeurism and child pornography in connection with videos that were found during a search of the home. Susan Powell's father has filed for custody of the children.