Ms Stewart said the area around the boy's body had been cordoned off.
"There's considerable work ahead of us as we begin our homicide investigation. Our investigation is likely to take some time as we build up a picture of the events that have led to this tragic outcome."
Ms Stewart said police would now focus on the homicide investigation and coronial process.
She again appealed to any members of the public who saw Alex and his adult brother Eric on or before Monday night to immediately contact police.
Police have confirmed the body was removed from the scene this evening and that the scene with be secured overnight.
A detailed examination of the area will continue tomorrow as part of the now underway homicide investigation.
Timeline of events in Alex Fisher disappearance
• MONDAY 6.15PM: Alex and his older brother Eric are seen at the Four Square dairy in Waitarere. • MONDAY NIGHT/TUESDAY MORNING: Alex is believed to have gone missing from the south side of Waitarere Forest, near the local domain. • TUESDAY 4AM: Alex's family, who live in Levin, report him missing. • TUESDAY 2PM: Police, along with Search and Rescue teams and dog units, search the Waitarere Forest for Alex. • TUESDAY - UNKNOWN: A man in his 20s is arrested in Forest Rd, Waitarere, charged with illegal possession of a knife. • TUESDAY NIGHT/WEDNESDAY MORNING: Searchers on foot continue looking for Alex. • WEDNESDAY 6.30AM: Police announce "items of interest" have been found during the search. • WEDNESDAY 9.30AM: A helicopter scours the coast as the search effort ramps up. • WEDNESDAY 12PM: Police announce they have found Alex's inhaler and his pencil case but say there's still no evidence of foul play. • WEDNESDAY 1PM: The search remains focussed on the South Block, which includes dense undergrowth. • WEDNESDAY 2PM: Police are seen distributing among themselves a CCTV photo of a man beside a young boy at a supermarket. • WEDNESDAY 3PM: A man appears in Levin District Court and is granted interim name suppression and remanded in custody after a brief hearing. • WEDNESDAY 5.30PM: Police reveal the footage seen earlier is of Alex and Eric. • THURSDAY 8.45AM: The search escalates, with 130 people joining efforts to find Alex. The Army deploys troops to join the search, transporting them in Light Armoured Vehicles. Searchers use a drone for the first time. Searchers focus on areas of bush not covered earlier. • THURSDAY 1PM: A helicopter crew see what appears to be a boy's body near Waitarere Beach. • THURSDAY 3.15PM: Police announce the body is believed to be Alex's. • THURSDAY 5PM: Forensic teams are seen near properties close to sand dunes. Police are seen at the back of an apparently uninhabited house about 300m south of the Surf Lifesaving Club, just a few blocks away from the Four Square.