I believe that this should be an option in the clan hall portion of the game.
For example, let's say ACad Doe is in Konoha's clan. He is tasked out to go do a mission and 'spy on' Amegakure (which is only a clan, and not a village).
In order for this to happen, ACad Doe would select an option that would be something like 'Visit another clan' or 'Talk to other clan' and then pick Amegakure.
This would send a request to the clan leader that Doe wants to visit and, just like adding a new clan member, he'd be allowed to hand out a visiting pass. Of course, if the leader of Ame finds out Doe's true intention, he could revoke the pass (should be done RP-wise, to make it more fun though
)
Kind of like giving out keys to dwellings, but people would have to request the keys instead of you just manually giving them away.