Mercedes says a leak inside the cooling system led to contamination in Nico Rosberg's power unit, which was why the team opted to change the engine.
Mercedes had brought an upgraded engine to this weekend's Italian Grand Prix but a problem was detected with Rosberg's unit after the third practice session on Saturday.
Mercedes had to revert back to an old specification engine for Rosberg ahead of qualifying, leaving the German driver down on power as he set the fourth fastest time.
The squad has now confirmed that there was no problem with the upgraded power unit.
"[The issue] was traced to a leak in the cooling system which contaminated the Power Unit, not a problem with the engine itself," Mercedes confirmed on Twitter.
"The Power Unit will be inspected in the coming days to decide if it can be used again at future races."