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What, if any, mechanisms prevent unauthorized commands? Asks what measures are taken for spacecraft, although the answer doesn't go much farther than pointing to the What would one need to do in order to hijack a satellite? question on Security.SE.
Similarly, Encryption in radio system asks about whether encryption is used in space, receiving a shuttle answer.

But when did they start using encryption, specifically for probes beyond Earth orbit?

Famously, Luna 9 sent its photos back to Earth in a standard fax format, enabling Jodrell Bank to receive the transmission. Although they were specifically asked by the Soviet Union to do so, clearly no encryption was used.

Encryption was poorly understood and quite the hassle back in the 60s. While that is not the case today, is listening/talking to deep space probes still just an issue of expensive equipment and obscure documentation? If not, when did that change?

SE - stop firing the good guys
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    Encryption was not poorly understood in the 60s at all. – GdD Nov 03 '20 at 17:13
  • Are you asking only about the radio links with the spacecraft, and not the terrestrial connections between facilities? – DrSheldon Nov 03 '20 at 19:01
  • @DrSheldon Not between terrestrial facilities. – SE - stop firing the good guys Nov 03 '20 at 19:04
  • The field of encryption (or cryptography) has existed since before antiquity and was (possibly still is) ahead general computer science. In fact, the Cuban missile crisis in 1962--at the height of the Cold War, which was a war defined by espionage and counter espionage all backed by cryptography. Saying they were "bad at encryption" is just wrong. – Dragongeek Nov 03 '20 at 21:10
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    I stand by this. Space travel predates fundamental concepts like key exchange and asymmetric encryption. Espionage before that is just silly cipher games. – SE - stop firing the good guys Nov 03 '20 at 21:36
  • Since first contact with the Fremulonians. – Chris B. Behrens Nov 03 '20 at 22:52
  • By deep space you mean probes beyond Earth orbit? Why would encryption for those be more critical than those in (low) Earth orbit? If anything, physical access to big antennas may make it less rather than more critical for remote interplanetary probes. – gerrit Nov 03 '20 at 23:00
  • @gerrit Yes, I mean probes beyond Earth orbit. I do not claim encryption is more critical for those (like you, I suspect the opposite), I'm merely limiting the scope to keep things like spy satellites and other "obvious" targets out of the way. Or put another way: the answer is probably different for deep space probes and Earth orbit probes, so I'm only asking about one of them. – SE - stop firing the good guys Nov 03 '20 at 23:33
  • @SE-stopfiringthegoodguys Then its possible that "civilian commercial & communications", "civilian science & Earth observation" and "military & government" may slice things up the way you want (functionally) better than the orbits do. – uhoh Nov 04 '20 at 03:10
  • I think the question to ask here is "Why?" What does encryption do for you in a space probe? It's more hardware and software to have to deal with in a place and situation where you try not to have anything excess to the mission. More stuff in space is just more stuff that can fail and leave your probe dead. – JRE Nov 04 '20 at 11:00
  • For a science probe then, even if you are worried about bad people taking it over you don't really need encryption: you need digital signatures. So if I send a set of commands, I sign them with some secret key I keep to myself, and the probe checks the signature before executing the commands. Comms the other way probably does not need anything more than sufficient error-detection/correction code wrapped around it (if even that). –  Nov 04 '20 at 17:36
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    Note that you can authenticate a message (i.e. ensure both the no modification and the identity of the emitter) without encrypting it (i.e. anyone can read the message and check its authenticity) – Manu H Nov 04 '20 at 20:07
  • @ManuH I would count that under a broad "encryption" umbrella here. – SE - stop firing the good guys Nov 04 '20 at 21:03
  • I believe all NASA missions are now required to encrypt their uplink, but I can't remember the guideline. Having said that, there is a good chance interplanetary may be exempt from this. Encryption adds significant overhead to the link, and when communicating at bits per second that overhead cannot be afforded. – Carlos N Nov 05 '20 at 03:59
  • @CarlosN I don't think there are any examples where a significant but not huge increase in the length of an uplink command would cause any problem. These things take days or weeks to plan and schedule and are pretty infrequent. – uhoh Nov 05 '20 at 22:51
  • @SE-stopfiringthegoodguys I would prefer "cryptographic tools". Encryption implies the message cannot be read by others. Yes this is a minor semantic issue but precision helps defining the scope of the question (e.g. what you call encryption includes cryptographic methods I don't consider as "encryption") – Manu H Nov 06 '20 at 09:41

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