The ministry statement added that the family of Ruben were among those who perished.
Officials said the boy's aunt and uncle flew from the Netherlands and arrived at the al-Khadra hospital in Tripoli, the capital of Libya, where Ruben was being kept under care.
The boy immediately recognised his loved ones and smiled at them when they came in, a Dutch Embassy spokeswoman on Thursday told NOS, a Dutch state broadcaster.
Jan Peter Balkenende, the Dutch prime minister, said that Dutch embassy officials in Libya were at the scene, gathering information and providing assistance.
The Libyan aircraft, which was on a regular flight from Johannesburg, crashed while attempting to land at the airport in Tripoli.
Aviation experts combed through debris for more clues on Thursday after finding the two black boxes from the Airbus jet.
Planemaker Airbus issued a statement confirming it had manufactured the plane involved in the crash.
"Airbus will provide full technical assistance to the authorities responsible for the investigation into the accident," it said.
The crashed aircraft was delivered from the production line in September 2009 and had accumulated about 1,600 flight hours in around 420 flights, Airbus said.
The aircraft is the same type as the Air France flight 447 that crashed in the Atlantic last year, on June 1. The cause of that crash has not been firmly identified.
Afriqiyah Airways executives said the crash was the first in the history of the airline, which was established in 2001.
Chris Yates, an aviation analyst, who talked to Al Jazeera from Manchester, UK said the fact that the aircraft is new makes the incident sort of mysterious.
"We are trying to put the picture together. There are two black boxes. One records data and one records voices and conversation with ground operations. There are a lot of data," Yates said.
"We are taking maintenance issues into consideration, but we can't rule out anything right now. It will take days until we have definite answers."