Hughes was set to join up with the League Two side but the clubs failed to complete the deal before the emergency window closed on Thursday afternoon.
Magpies chief executive Jim Rodwell told the club's official website: "As a football club, Notts County do not have the luxury of reporting on speculation or gossip, we only deal with facts.
"A proposed loan deal for Lee Hughes to go to Port Vale was discussed, however as it was so late in the day, the paperwork did not go through in time and we are delighted to confirm that Lee remains a Notts County player.
"We have been widely criticised on various social media sites for not commenting on newspaper reports but this is exactly why we do not make public statements until everything is signed and sealed."
The veteran forward begins a three-match suspension this weekend after being charged by the Football Association for an incident in their match at Scunthorpe last weekend.