Army commandos stormed the mosque complex in July last year after a week-long stand-off with well-armed militants and their supporters who refused to surrender to authorities after violence erupted outside the mosque.
More than 100 including students were killed.
Troops recovered weapons in the complex, and showed them off to reporters after the assault.
The weapons were then stored at a nearby police station but had gone missing, said Interior Ministry spokesman, Shahidullah Baig.
"Over the passage of time, the weapons have been stolen. It did not happen in a day," Baig said.
Ten policemen, including the head of the police station where the cache had been stored, had been arrested and an investigation had been launched, he said.
Baig declined to say what kind of weapons had been stolen.
Last Mod: 22 Aralık 2008, 16:37