Italy's Health Minister Beatrice Lorenzin slammed the "intimidatory act" on the European Food Safety Authority (EFSA) in Parma after the parcel bomb was found in the post room.
It "calls for swift action from all investigative forces to throw light on what happened," she said.
"I strongly condemn the vile act and express my deep sympathy with all of the employees at the Parma offices," she added.
The alarm was sounded after the package was found to be addressed to someone who does not work at EFSA. An X-ray revealed it contained a battery and wires, local daily Gazzetta di Parma said.
The security service at the postal sorting centre of the European agency's headquarters alerted the police and bomb disposal experts were called in, detonating the device in a small square near the EFSA building.
Prosecutors in Bologna have launched a probe into the bomb, which investigators said was likely to have exploded or ignited on opening.
"Science will not be intimidated," EU Commissioner for Health and Food Safety, Vytenis Andriukaitis, said on Twitter.