The reform is one of a series of far-reaching changes adding up to a fundamental shift in the balance of power within the Commission.
The moves are designed to buttress the role of the Commission President at the expense of individual commissioners, who will in future work like ministers in a government, rather than as a 20- strong "college of equals".
Up to 1,000 staff will spend the summer moving from the Breydel building in the centre of Brussels to make room for Mr Prodi's command centre. As the "centre" is strengthened, commissioners - who now have their private offices in the Breydel - will be scattered around the city. They are also due to be deprived of their personal press officers in an attempt to force the Brussels information system to serve the Commission rather than individuals.
Mr Prodi has decided to tighten his grip on policy too, in order to give sharper focus to the two areas he wants to develop under his leadership: Balkan reconstruction, and job creation throughout the 15-member bloc - possibly with a new employment pact. And his decision to make his two vice-presidents responsible for EU reform, rather than giving them the expected portfolios covering economic and foreign policy, has opened the way for Mr Prodi to take ultimate control of these areas.
Allies insist that the new President will use his authority to push forward with European integration. A source close to Mr Prodi said: "He believes in a united Europe which is more than a single, commercially united area. He believes in an EU common foreign policy and monetary policy, and in the political role of the Commission. But he does not believe in an approach which destroys national identities."
Mr Prodi's arrival marks a real desire to achieve change. But some colleagues remain sceptical about his ability to centralise power in the way that prime ministers can.