The images had appeared in an internal training session, Greater Manchester Police (GMP) said.
Assistant Chief Constable Debbie Ford said: "The fact that we believe these images have been used again is totally unacceptable."
GMP apologised in June for using a "distressing" photo of Hillsborough.
Ninety-six Liverpool fans died as a result of the disaster at the 1989 FA Cup semi-final at the Sheffield football ground.
Ms Ford added: "I have written to the families of the Hillsborough victims to apologise for the distress this may cause them.
"I have also taken steps to prevent this from happening again, which includes suspending work around the super recogniser programme until 2017 while the necessary measures are taken to remove any inappropriate images."
The photograph that led to GMP's apology in June was used on a poster advertising for 'Super Recognisers', who are skilled at picking out faces in a crowd.
GMP said it accepted that the use of images from the Hillsborough disaster was "totally inappropriate".
It said staff were told that "using these images in any format is prohibited".
Louise Brookes, sister of Andrew Brookes, who died in the Hillsborough disaster aged 26, said in June she was told the photograph showed one of the pens where the fatal crush occurred.
A police officer has been suspended on suspicion of gross misconduct over the alleged misuse of images of the Hillsborough disaster.