IS claimed responsibility for the attacks across Paris on November 13 and the suicide bombings in Brussels on March 22.
"We know that the orders came from the Islamic State zone.... We know that it went very high in the command," Frederic Van Leeuw said in an interview with AFP in Brussels.
He could not say exactly who gave the orders or whether they sent them from a base in Syria or Iraq, the territory run by IS leader and self-declared caliph Abu Bakr al-Baghdadi.
He said the command moved around to dodge US-backed strikes. "Baghdadi was for a while in Mosul (Iraq), sometimes in Raqa (Syria)," he added.
"We don't know at all who are the people who really gave the orders," he said.
IS claimed responsibility for the attacks across Paris on November 13 last year that killed 130 people as well as for the suicide bombings at Brussels airport and a metro station on March 22 that killed 32 people.
Van Leeuw said the attacks were carried out by the same Franco-Belgian cell in which "the logisticians in one case became the operational ones in the following case".
With authorities still looking for suspects, he added: "The investigation is far from having ended, as much at the Belgian as at the French level."
French sources told AFP on Tuesday that French investigators had identified Oussama Atar, a Moroccan-Belgian jihadist based in Syria, as a "coordinator" of attacks in Paris and Brussels.
Van Leeuw said Atar's suspected role "is one of the working theories among others. There are a whole series of checks to be done".
Atar, believed to go by the pseudonym "Abou Ahmad" in Syria, has been on the radar of European security forces for more than a decade.
Abou Ahmad is suspected of having sent two suicide bombers to the national stadium in Paris as well as another pair of potential assailants, who were delayed on their way to Paris and arrested in Austria in December.
After being arrested in Iraq in 2004 following the US-led invasion of the country, Atar spent time in various jails including the notorious Abu Ghraib prison used by American forces.
After being released, in 2012 he returned to Belgium before apparently making his way back to the Middle East but intelligence services lost track of him months ago.
Asked why Atar had not been under surveillance, the prosecutor said even the French, who had more manpower, could not monitor someone round the clock.
"We must abandon this idea that is possible to follow people 24 hours a day... even when a legal case is opened," he said.
Van Leuw said Belgium had made "enormous progress" in the investigation into the attacks.
"The goal is effectively to understand and retrace everything that happened before, to retrace the entire chain of command," he said, adding that much police work lay ahead.