"As a dad you feel sick, it's an incredibly distressing thing that has happened, and on behalf of everybody across our state I echo to her friends and to her family that our hearts break when you hear that news," he told the Nine network on Thursday.
"It's never easy and the whole thing has been incredibly sad and tragic."
A vigil celebrating Charlise's life was held on Wednesday night at Tweed Heads, near the Queensland-NSW border.
Locals left bouquets of flowers and messages outside the gates of Tweed Heads Public School where Charlise had been a student.
About 150 people had gathered, staying on despite light rain.
A message on the school's notice board read: "Don't count the days, make the days count."
The school released a statement on Wednesday that it was "absolutely devastated" by the girl's death.
"Charlise was a much loved member of our school who brightened all our days, every day," the statement read.
The school shared a recent photo of Charlise holding a literacy award she received at their end-of-year presentation day.
Prime Minister Scott Morrison said his thoughts were with the family after the unfortunate end to the search for the missing girl.
"You hope for the best, you pray for it, but it doesn't always occur," Mr Morrison said.
The grim discovery of a child's body in a barrel dumped near the Colo River came after a five-day search of bushland was conducted around the Wildenstein Private Gardens at Mount Wilson, where Charlise had last been seen alive.
Justin Stein, 31, faced court on Wednesday charged with murder after being arrested at a Surry Hills unit.
Police analysed CCTV and GPS data to narrow down their search to an area near the Colo River, alleging Stein had allegedly tried to float a boat at an inner-Sydney dock after purchasing sandbags from a hardware store, before travelling back to the Colo River.
Investigations are ongoing, with police yet to determine how she died or any motive for her murder.
Stein will remain behind bars until the case is due back in court on March 18 in Penrith.
