Normally the government (in this case Iran) contacts the service provider (in this case FB/Whatsapp)and lets them know that unless they self-block their service, the government will do blocking at the network level and might issue fines.
Normally, that makes the service provider implement blocks on their end, because then at least they can present the user with a sensible error message, and other services that the government isn't trying to block are not impacted (eg. services hosted on the same servers - for example Whatsapp voice calls might be banned, but text chat not banned).
Normally, that makes the service provider implement blocks on their end, because then at least they can present the user with a sensible error message, and other services that the government isn't trying to block are not impacted (eg. services hosted on the same servers - for example Whatsapp voice calls might be banned, but text chat not banned).