The charge comes after Scunthorpe asked the governing body to review the video of the League One fixture between the two clubs at Glanford Park last Saturday, when Hughes is shown to elbow home defender Tom Newey.
Iron boss Brian Laws was furious the 36-year-old forward was not punished by match referee Eddie Ilderton at the time, calling the incident "clear".
Hughes went on to score a late goal to rescue a 2-2 draw for his side, having also scored in the first half.
He will now miss the Magpies' league games against Swindon and Yeovil and also their FA Cup second-round tie against Rotherham.
