While the main thematic issues of Code 46 are hardly new or surprising, (although the relatively evenhanded way in which it tackles them is novel), the way it portrays its state and its control is unusually nuanced. Unlike many other tales of dystopian governments the state is abstracted from human beings. Similarly the way it maintains control over its populace is subtle and calls to mind the theory of governmentally. Finally its sexism, while not commented on directly in the film, is insidious.
The state in Code 46 is not associated with one human being. There is no dictator, no Emperor Palpatine on whom we can pin the malevolence of the government. Indeed there isn't even a government suggested or shown to absorb our outrage. Oppression is not the work of one man in Code 46, rather it is the result of the employees of the state who have internalised the discourses on which its control rests.
Code 46 gives us some remarkable sketches of government bureaucrats. Despite limited screen time each one is given as distinct a personality as possible. There's the warm, slightly shy woman at the company who is determined to be as polite as possible, the man with learning difficulties and the bored woman pissed off at her work. Yet despite their individuality they, and their less remarkable compatriot at the gene center, are determined to keep to their script and follow their processes - no matter how much sympathy they may have for Robbin's character. They have a job to do and they will do it to the letter, even small and ultimately harmless disturbances such as Robbin dodging the normal entry procedures for the Papel company are unwelcome deviations that put their jobs, and their ordered lives, in danger.
The occasional, undramatic, shifts to the POV of a security camera remind us that these characters are being watched. And they know it. Should some slip-up occur there is always the possibility that someone could go back through that footage and find them wanting. However this is more a subtle, cheap threat then the clear and present danger it turns out to be in many other films. There are no scenes of government agents watching the footage - no one needs to waste the money employing such persons when the threat is enough.
A similarly subtle threat is the presence of those on the outside. For a society so concerned with the welfare of its citizens it might seem odd that the government chooses to let these people languish outside the metropolises with only their ability to make do and sell trinkets to those on the inside. These people serve as a warning for those under the protection of the state - if you don't live by our laws you won't receive our benefits and this is what happens to those not under our protection.
And those most likely to be punished for their transgressions would appear to be women and lower class workers. It takes two people to create a fetus and yet it is Morton's character who bears the brunt of both punishments - she has the memory of the affair wiped from her mind and her fetus aborted. He, on the other hand, is not even given an explicit warning. Similarly he, the initiator of their second round of civil disobedience, whose breaking of laws was caught on camera, is judged simply to have misplaced his judgement, while she is exiled. The film never lays out explicitly whether the difference in their treatment is the result of her class or sex and its difficult to untangle the two: certainly the degree of control exercised over Morton's body would suggest the latter, but in Robbin's treatment there are intimations of the former - one suspects both played a role.
The laws of Code 46's society are not enforced by expensive, inefficient tools such as thugs in uniform, indeed the movie goes out of its way to remove any traces of the government agents who presumably investigated the case, arrested Morton and retrieved the lovers from the car crash. Instead control is maintained in a more Orwellian way: by ideas of how society is to be run and how citizens are to behave that are deeply ingrained.