The helicopter crashed shortly after take-off early yesterday, killing three of the 10 people on board instantly and injuring the toddler, who died later in hospital, military sources said.
All six surviving passengers are being treated for serious injuries.
Defence minister Nahas Angula said the helicopter failed to gain altitude and crashed at the end of the runway and burst into flames.
The minister refused to confirm or deny reports the helicopter was en route to the capital Windhoek to pick him up and take him to an air force graduation ceremony.
Angula said an investigation into the accident had been launched.