The airport said routine baggage screening had revealed "a bag which appeared to contain a suspicious item".
Hundreds of passengers were ushered out of Terminal 3 as a bomb disposal team was called in to investigate.
The Greater Manchester Police force said bomb disposal officers conducted a series of controlled explosions on the bag. The force said "the package is not believed to be a viable device,'' and the incident was not terrorism-related.
The two other terminals at the northwest England airport remained open, and aeroplanes continued to take off and land after the evacuation.
The airport said passengers due to fly from Terminal 3 should contact their airline.
