WDIV-TV reports John Skelton said those are not his "boys" when asked about the remains during an interview at a Michigan prison where he is serving 10 to 15 years for unlawful imprisonment.
Andrew, Alexander and Tanner Skelton were 9, 7 and 5 when they were last seen in 2010. Skelton failed to return them to his estranged wife in southern Michigan on Thanksgiving.
Skelton has said he gave the boys to a group to protect them from their mother.
DNA testing is being done on the remains.
Sgt. Travis Welsh says Missoula detectives have not spoken with Skelton, and there's "no known connection" to the boys' disappearance.