The boy's parents discovered that their child was missing after life guard surveillance had ended on the beach at the West Flemish resort.
They alerted the emergency services and a sea recue operation was started.
A police helicopter discovered the youngster 150 metres off the coast. The boy was taken to hospital in a serious condition and died the following morning.
The governor's move follows a complaint by one of the emergency services claiming that sea rescue services only arrived at the scene one hour after the child's mother first raised the alarm. It's also claimed that communication with the air force base at Koksijde that operates Seaking rescue helicopters did not go smoothly either.
Mr Breyne: "We will investigate if all services operated as they should have. The focus of the investigation will be on the speed of the operation and communication channels."