The package, found in the offices of the new EU External Affairs Commissioner Chris Patten, contained an alarm clock wired to a plastic bag filled with a substance resembling plastic explosives.
"First indications are this was a fairly convincing attempt at a bomb hoax," said EU spokesman Steve Morris. "The device is being examined to see if it has some sort of innocent explanation."
Morris said the possible bomb hoax was taken "very seriously" because Patten was the main author of a controversial report on police reforms in Northern Ireland released just before he took over as EU commissioner last week.
Patten was in New York on Thursday for the meeting of the U.N. General Assembly.
Morris said the EU Commission had received no bomb threats and no message was found with the device. He said it was discovered by one of Patten's secretaries among packages sent to the new commissioner from the offices of Sir Leon Britten, the former EU trade commissioner who left office last week.
Since the device was in packages apparently sent through the internal postal system of the EU civil service, it was not subjected to the X-ray and metal detection checks applied to mail coming from outside, Morris told reporters.
Belgian police evacuated hundreds of staff from the "Charlemagne" building, a 17-floor glass-and-steel office bloc that is home to the Commission's foreign policy services. Staff were allowed back into their offices about two hours after the evacuation.