Dylan Redwine went missing in November 2012 while on a court-ordered visit with his father, Mark, in Colorado.
The child's remains were found seven months later scattered in southwestern Colorado mountains by wild animals.
Prosecutors now say that Redwine may have killed Dylan after he was confronted about the "disturbing" pictures.
Redwine was arrested on Saturday and indicted by a grand jury with charges of second-degree murder and child abuse resulting in death after the four-and-a-half-year investigation.
Redwine has constantly denied playing a role in his son's death and at one point appeared on Dr Phil to blame his ex-wife for the child's death.
Cory Redwine, Dylan's older brother, revealed that he had seen the photos.
"I have seen the photos. It shows him wearing women's clothes and makeup and a diaper and then eating his feces from the diaper. It was disgusting. We couldn't believe it," he told .
Dylan's mother, Elaine Hall, added that she believes her son confronted her ex-husband about the photos and was murdered for it.
"He may have said something that just didn't set well with Mark and Mark reacted in a very violent way…obviously. Dylan is no longer here," Hall said on a February 2015 podcast.
Redwine is being held in Bellingham, Washington, on a $1million bond and is facing extradition to Colorado, the reported.
However, the issue of whether he will fight extradition will be decided at a later date after confusion over whether Redwine was offered his right to waive the hearing.
BLOOD IN MANY LOCATIONS
On Monday, the court was given an outline of the charges against him and bail was set.
In the grand jury indictment, investigators said blood was found in multiple locations in Redwine's living room, including his couch.
Cadaver dogs even found the scent of a dead body in various locations in the home and on the clothes Redwine wore the night Dylan disappeared, the indictment says.
In 2014, the cadaver dog also picked up the scent of a body in the bed of Redwine's pickup truck, according to the indictment.
Authorities also said Redwine had mentioned how investigators would have to find his son's skull before they determined how the teen died.
Dylan lived north of Colorado Springs with his mother but went to his father's home near Vallecito Reservoir northeast of Durango for a court-ordered visit in November 2012.
His dad said he returned home from doing errands to find his son had gone. The two parents subsequently blamed each other for their son's disappearance.
But in June 2013, Dylan's partial remains were found on Middle Mountain.
Hikers found his skull 1.5miles away in November 2015, according to .
Investigators said Dylan's skull was found in difficult terrain that was easily accessible by a road that Redwine was very familiar with.
The skull had injuries consistent with blunt force trauma and two small markings that appeared to be tool marks from a knife, the indictment alleges.
Months after the first remains were found in 2013, Hall said she believed her ex-husband killed Dylan.
"I always have from day one, when he was missing," she told The Pine River Times at the time.
According to the indictment, Dylan had not been getting along with his father prior to his disappearance as he watched his two parents in the midst of a bitter divorce and custody battle.
Hall told authorities that her ex-husband told her he would "kill the kids before he let her have them", the indictment alleges.
On Wednesday, police released body camera footage of Redwine being arrested.
The video shows police approach Redwine's truck with their guns drawn, giving instructions over a loudspeaker for him to leave the truck and get down on the ground, which he did.
Then Redwine, wearing a red T-shirt and a baseball cap, can be seen in the footage lying on his stomach with his hands by his head before police handcuff him.
Later in the nine-minute video, they tell him he is being arrested in connection with a warrant for second degree murder.
-Dailymail