Four of the pictures, which showed William and his fellow servicemen in front of computers, had sensitive information visible on the computer screens. They had been put up by mistake on the website before being cleared.
The "administrative error" meant that the Ministry of Defence had to reset the username and passwords of several RAF staff. The pictures were removed from the website one the mistake was realised, but by then they had appeared on TV, in newspapers and online. The photos were then re-released with the sensitive information pixelated.
In one of the images the Duke can be seen sitting at a computer with a document next to him that can be read clearly. An email is open on the computer behind him and an iPhone is by his side.
An another, William is joking with his fellow servicemen in front of a computer with a password prompt screen open.
An MoD spokesperson said: "Due to an administrative oversight, these photographs were not properly cleared at RAF Valley and the images showed unclassified MoD user names, passwords and computer screens on a restricted system.
The passwords and user names shown have now been reset as a precaution and we are satisfied the images do not contravene security regulations. All the photos have been now amended and reissued."
A St James spokesperson added: "The pictures were taken by an RAF photographer and any security issues are a matter for the MoD. Four of the pictures had to be taken down for a period.
The photos gave a rare glimpse into a typical 24-shift for the second in line. An accompanying explanation told how "Flt Lt Wales’s shifts are the same as any other pilot." It adds: "During the shift, the crew is constantly on-call. Even while airborne on a training flight, they can be called to perform a rescue. Like the civilian emergency services, the type of incident varies tremendously. It could be anything from rescuing a group of lost hill walkers in Snowdonia to a large-scale operation rescuing people from a sinking vessel out in the Irish Sea.
William and his colleagues like to relax during their downtime by playing computer games. The report says: "Tthe likes of ‘Call of Duty’ and other military-themed games – are a favourite for the crew if they have a spare moment in the evenings. However, they must remain in constant contact and can never be more than 60 seconds away from their aircraft in case an emergency call comes in."