The Commission and External Action Service experienced a "serious" cyber attack as officials were preparing for an E.U. summit in Brussels to discuss the future of the union's structure and unified operations in regards to multiple global political events.
Details of the incident have not been divulged, but officials consider the event to be of sufficient magnitude to necessitate several strict defensive measures.
"The Commission and External Advisory Service are subject to a serious cyber attack. We are already taking urgent measures to tackle this. An inquiry's been launched. This isn't unusual as the commission is frequently targeted," said the security and information technology commissioner's spokesman Antony Gravili.
The Commission has disabled email access to the affected networks, as well as the staff intranet system to prevent the loss of sensitive information.
"We're often hit by cyber attacks but this is a big one," a source told BBC News.
The event is reminiscent of an attack suffered by the French Finance Ministry in December.
In that incident, 150 computers were affected in what was thought to be an effort to harvest sensitive information about the G20 Summit that took place in Paris last month.
It is unclear at this point in the investigation whether the latest attack was connected to the upcoming E.U. summit.