He asked for Roberts to be remanded in custody without plea to the High Court in Christchurch on June 19.
Judge Tony Couch declined applications by media to film and take photographs of Roberts today as police investigations were ongoing.
Neither police nor Mr Cook made applications for name suppression.
As Roberts was being led back into custody, a friend of Leon's father shouted from the public gallery that he had a message for him.
"Rot in jail," he yelled before storming out of court.
Leon will be laid to rest at a "remembrance and farewell for our special wee dude" at Avonhead Baptist Church in Christchurch today at 1pm.
A death notice published yesterday paid tribute to "our little superman was tragically taken from us, surrounded by his loving family and trusty sidekicks".
"Treasured, adored and greatly loved son of Emma and James, chief mischief maker of his brothers and sisters Lucas, Nadia, Anabelle, Fabian, and Liam; Giane, Daniel, and James," it said.
A Givealittle page set up last week to help the family with the funeral expenses has so far raised more than $3800.
A scene examination of a Papanui house was completed on Saturday evening.
Officers seized a number of items for forensic examination.
A post-mortem examination was carried out on Friday.
"While the investigation will continue to focus on the events of May 27, 2015 we are also working with other government agencies to build a full picture of what has led to this tragic event," Detective Senior Sergeant Scott Anderson said yesterday.
Mr Anderson said police would "work tirelessly to ascertain why a 'normal' day for Leon ended as it did".
