Symfony2 $user->setPassword() updates password as plain text [DataFixtures + FOSUserBundle]

Since you are using FOSUserBundle, you can use UserManager to do this. I would use this code (assuming you have $this->container set):

public function load(ObjectManager $manager)
{
    $userManager = $this->container->get('fos_user.user_manager');

    $userAdmin = $userManager->createUser();

    $userAdmin->setUsername('System');
    $userAdmin->setEmail('system@example.com');
    $userAdmin->setPlainPassword('test');
    $userAdmin->setEnabled(true);

    $userManager->updateUser($userAdmin, true);
}