I don't know what the actual procedure is; however like with Science Fiction and 'Self Destruct' codes I would think that a multi-agent auth challenge would be required.

The captain and some fixed number of executive officers. Possibly with redundancy for one or two crew being dead. The auth codes would cause a safe to unlock or message to de-crypt.

Presumably the instructions would be delivered to each authenticating member so that all could receive the orders simultaneously.