Hmmm. Well, follow my thinking here for a minute.
Since the villages are sorta equivalent to nations they'd each have their own specials ops teams and clans like the real world equivalents of the FBI and CIA and all those agencies.
On the other hand, they'd also act with diplomatic relationships in mind. Since Kiro is a ninja from the Hidden Mist, then he's basically one of them and would receive their protection. They wouldn't be able to throw the bulk of their forces at him because that'd be the same as declaring war on the mist. They might, however, try to assassinate him. But once he gets back to the hidden mist he's basically untouchable.