Among the missing items are some 5,800 pounds worth of the anti-impotence pills, which the forces use for treating altitude sickness.
A replica AK-47 assault rifle -- which was later recovered -- 100 bayonets, gun parts and thousands of rounds of live and blank ammunition have also vanished, The Times newspaper reported.
An aircraft fuselage, a truck, a karaoke rig and a pulse oximeter, which measures blood oxygen saturation, from the nuclear submarine HMS Ambush also disappeared, the daily said.
"There are robust processes in place to raise awareness of the need for vigilance in all aspects of security, but just as theft occurs in wider society, the MoD is not immune and we actively encourage individuals to report any evidence of loss or suspicion of theft."
The ministry set up a counter-fraud and loss department last year. Around 600,000 pounds of stock has been recovered.