The body of a boy believed to be Alex Fisher has been found.
Inspector Sarah Stewart said a homicide investigation was now underway.
The boy's body was seen in the Waitarere Beach area, spotted by a helicopter at around 1pm.
A ground search team found his body.
Alex's family were "devastated by the news," Inspector Sarah Stewart said.
"Obviously this is absolutely the worst outcome."
The cause of the boy's death was yet to be established.
Earlier, authorities ramped up the search at Waitarere near Levin, deploying helicopters, a drone and roughly doubling the search team to some 130 people.
At that point, Alex's location remained a mystery, despite the arrest of a man allegedly linked to his disappearance.
A resident who lives a few doors down from Alex's home in Levin described the missing boy.
"He is not troubled at all. He's just a normal happy boy. He's always smiling, always polite. His parents love him to bits. He's their baby."
Alex was a student at Ohau school, she told the Manawatu Guardian.
Some 10km away, search teams including police have been visiting properties not only around Waitarere Domain, where Alex went missing, but across the town of about 500 people.
Manawatu area commander Inspector Sarah Stewart said hundreds of properties were being visited, and gardens searched.
At this point the focus was not on searching inside houses, she said.
"We're going through every single property and we're using Waitarere beach wardens, community patrols and our police to help us with that."
Police were still treating the operation as one of search and rescue, and had not given up hope of finding Alex alive, Ms Stewart said.
In fact, she said police weren't ruling out the chances of Alex being inside a local property.
But more than 60 hours after Alex went missing, there were serious, growing concerns for his health and safety.
Alex's family had a message for him, Inspector Stewart said.
"Your family are really worried about you. They're helping police to try and find you."
The family had been "incredible", she said, and had helped with the search.
"They're so upset and so worried about Alex and doing everything they can."
Seven army vehicles including five light armoured vehicles arrived from the army base at Linton to drop off Defence Force personnel on Forest Rd, near the entrance to the South Block search area this morning.
The Defence Force has also brought at least one more dog to the scene.
Ms Stewart said the Defence Force also brought along specialist trackers to help with the search.
A drone and a Rangitikei Helicopters machine were also deployed to help with the search today.
The search area has expanded from the Waitarere Forest South Block, with the helicopter seen over North Block, which one local resident said covered 2500 hectares.
Police are asking anybody who saw Alex with his adult brother Eric on Monday, or before, to come forward.