Central Scotland police confirmed the destruction had taken place, but gave no details.
The weapons, which have been in police hands since the massacre on 13 March last year, are thought to have been destroyed yesterday.
They included the semi- automatic Browning pistol which Hamilton used to kill his victims, and the revolver with which he then took his own life in the primary school gym.
The weapons had been kept for the Cullen inquiry, and then for the fatal accident inquiry into the murdered teacher Gwen Mayor on 28 November.
Weapons of that type are illegal since new gun control legislation inspired by the massacre went on to the statute book on 27 February, although the implementation of the ban and compensation measures are still being finalised.
Michael Currie, the Central Scotland deputy chief constable, said last night: "For security reasons I am unable to disclose what our arrangements are.
"The process that we use totally destroys firearms and ensures that they can never be used again. Thomas Hamilton's firearms have been destroyed. They will never be used again."Reuse content