Estava bastante bem escondido na burocracia burocrática. Jedi não eram exatamente advogados - eles estavam ocupados demais lutando em uma guerra.
Wikia diz:
Order 66 could be found in the document entitled Contingency Orders for the Grand Army of the Republic: Order Initiation, Orders 1 through 150, GAR Document CO(CL) 56-95, a document containing a series of special contingency orders that covered any and all emergency situations, which the clones that comprised the GAR were prepared to execute, immediately and without question, and only in specific cases of extreme necessity. Some of these orders concerned contingencies any armed force could conceivably face. Many dealt with contingencies specifically involving the GAR Supreme Commander — in this case, Supreme Chancellor Palpatine — and the effect on the chain of command were he ever to become incapacitated or declared unfit to issue orders. In particular, Order 65 dealt with the detainment and possible execution of the Supreme Chancellor by the Republic, further hiding the true intention of Order 66. Sufficiently buried among the other one hundred forty-nine orders so as to almost escape notice, Contingency Order 66 specifically dealt with the effect on the chain of command were issues to arise involving the Jedi.
No que diz respeito aos Jedi, a maioria das tropas não foi exatamente informada sobre o significado dessa ordem precisa, apenas uma lavagem cerebral para seguir qualquer ordem. Então, até que fosse dado, os Jedi não teriam percebido nenhum perigo de seus clone troopers / commanders (os Jedi não são exatamente leitores de mentes).