Sifo-Dyas was the only Jedi to know of the chips’ existence. Upon his death, only those who were involved from the beginning of the cloning program, such as the newly fallen Sith apprentice Tyranus, Sith Master Sidious and such key Kaminoans as Lama Su and Nala Se, knew of the chip’s true purpose, and they sought to suppress any knowledge of it. The chips were subsequently supplied by Tyranus, whose involvement remained a closely guarded secret by the Kaminoan leadership. The Kaminoans themselves apparently believed Tyranus to be a secretive member of the Jedi Order, even though through his directives they actively kept the nature of the chips from being known by anyone else.
Around 20 BBY, the chip of the trooper “Tup” malfunctioned, causing his Jedi-killing protocol to activate prematurely. Another clone nicknamed “Fives” ended up discovering the truth about the inhibitor chip, but he was framed for attempting to assassinate Supreme Chancellor Palpatine and was shot by one of his fellow clones before he could reveal it.
It was only towards the end of the Clone Wars that the Jedi learned the elusive figure they had identified as Tyranus was in fact Count Dooku. This led to the realization that the Sith had been involved in the cloning program from its inception, although they knew not to what purpose. They chose to keep this knowledge a secret from the Senate, as they thought it would destabilize the Republic and undermine the war effort. Instead, they resolved to take the only path they could see available, which was to play the game they now knew to have been orchestrated by the Sith, and bring an end to the war as quickly as possible.