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In episodes 1-4 of season 6 of Star Wars: The Clone Wars, the Kaminoans take direct orders from Count Dooku (as Tyranus). These orders conflict with the wishes of the Jedi, specifically Jedi Master Shaak Ti's. Why do the Kaminoans follow Dooku's directives, rather than Shaak Ti's? Why do they deliberately deceive the Jedi?

It is clear that Jedi Master Sifo-Dyas gave the order to create the Clone Army. It seems that the Sith intervened at some point, which may have been "with the change in motive unbeknownst to the Kaminoans", but why would they take orders from Dooku rather than Shaak Ti when given the choice?

I am looking primarily for an answer within the 2014 continuity reboot, though Legends sources could of course be used for speculation.

I just finished watching all seven seasons of the clone wars. So maybe I can shed some light.
(warning: some fairly heavy spoilers for season 7 ahead)

The sith were in league with the Kaminoans from pretty much the start. The only jedi that was involved (up until Obi-wan met with them) was Sifo-Dyas. Sifo-Dyas ordered the production of the clone army without the permission of the Jedi council, as He had foreseen a great conflict and made plans for the republic to be prepared.

In the Legends material, Sifo-Dyas' army was funded by Hego Damask, aka Darth Plagueis, Palpatine's sith master.

Sometime after Sifo-Dyas met with the Kaminoans, Dooku intercepted.

By killing Sifo-Dyas, with him out of the way...

Dooku then hired Mandalorian Jedi Hunter, Jango Fett, to be the template of the clones. Later, he gave the plans to have all clones be given an inhibitor chip to make them execute order 66 and kill the jedi.

It's safe to assume that for the 10 years it took to grow the army, the sith were the only ones overlooking the production of the clones.

The sith also were not a force that you wanted to disobey, especially when they were the ones funding the whole thing. Furthermore, the Kaminoans didn't care who they were working for; they were more neutral, not specifically on the jedi's side (who they viewed as simply clients). There is enough evidence that the kaminoans cared more about money than about the lives of anyone.

It's also to note that in those specific episodes, only a few Kaminoans knew about the siths involvement. The few that did were the higher ups: Nala Se (the prime minister), and Nala Su (a medical technician). It wouldn't have been hard for Dooku to bribe or threaten them.

Actually, they are not so much in it for the money as they are for the scientific knowledge and freedom that this war grants them. They get to create a clone army, train them, teach them from day one how to be a better soldier than the previous batch, study them for scientific purposes - I mean look at our society and how we look at the cloned sheep Dolly (http://www.animalresearch.info/en/medical-advances/timeline/cloning-dolly-the-sheep/).

Look at their facilities. They are bare, white, medical and scientific. They aren't in it for glamour or glory. They want knowledge. Remember how they wanted to kill Tup and dissect him for more information? They treated him like an experiment, not a human being.

They listened to the sith because the sith let them have as much scientific freedom as they wished, because the sith didn't care about the science experiments being fair or humane. The jedi would have though... and this is why they listened to the sith.

I dont think the kamioans fully knew who lord tyrannus was. In season 6 episode 2, after a transmission between tyrannus and nala se, nala se looks to the doctor near him and says "these jedi are a curious cult." Tyrannus also stated that the inhibitor chips were to protect against rogue jedi, but that the jedi were not allowed to know about it. I believe the kaminoans simply didn't care, as long as they were being paid.

I believe that douku was still acting as a Jedi when the clone's where ordered, so the kaminoans didn't think he was going to use the clones for evil. Also I don't think that the kaminoans exactly knew what the order 66 chip would do, but they still installed it.