Police issued the Amber Alert just before midnight last night, six hours after the boys were last seen in the Townsville suburb of Cranbrook leaving their home on Brett St.
CCTV from a neighbouring house caught the two boys walking down the street around 5.30pm yesterday with the older boy wearing a local school shirt that was red with white sleeves and the other wearing blue shirts with no shirt.
Both boys were described as Aboriginal.
The boys were filmed walking to their favourite park just before 4.30pm before disappearing from view.
"The boys apparently are regular visitors to the park but they haven't come home at their usual time so family started looking for them," Townsville Police District Duty Officer Senior Sergeant Ian Wilkie told reporters.
"When they were unsuccessful they contacted police."
The police helicopter spent the night searching while officers on motorbikes and on foot searched the nearby Ross River and neighbouring suburbs. Water Police also joined the search down the river.
In the Amber Alert issued, police urged residents from Condon to Rosslea along the river to check their backyards and be on the lookout for the boys.
Yesterday Sen-Sargeant Wilkie said police, as well as SES and any local volunteers, would spend the night conducting a "methodical search".
"That will continue until we are satisfied those areas have been covered," he said.
"If the boys aren't located tonight that search will continue for as long as required."
"We do believe that the boys, given their age, are quite possibly frightened and that they are small, (and) they are curled up somewhere.
"Certainly we are looking at every aspect of it but we are hopeful that they will be found overnight or early (Tuesday)."
More than a hundred Townsville residents, fearing for the boys' safety, joined the search last night.
One local told the Townsville Bulletinshe hadn't been able to sleep knowing they were out there alone.
"I've been out here for about an hour and a half," one woman told the publication.
"Police came and knocked on my door and asked us if we had seen any children and could they check the perimeter of the house.
"They showed us photos of the children — a three and a five-year-old.
"Being a grandmother I have a five-year-old grandson. I couldn't go to bed and sleep on it so I got out and helped."