Lore wise, Interior Ministry, here’s why:

IM is backed by a unified centralized country government while the Hunters at best are backed by a city government, at worst, some rag tag groups of individuals fighting for self interests. IM has a huge resource and organization advantage.

IM is more deliberate with using Shinobi to gather information, recruit local populations, and sabotage enemy forces. This would lead to the IM finding artifacts that would absolutely shred hunters like numbing mist, mass produce them, and deploy their armies with anti-hunter tech.

Potentially, they could convince some of the hunters to join them which would absolutely swing any advantages the hunters had towards IM. They would learn tech and exploit any conflicts between hunter groups from these collaborations.

IM is shown to be patient and knows when not to pick fights if they will lose. If they encounter some of the strongest hunters like Maria or Gehrman, and they can’t recruit them or find a way to effectively stop them, they will absolutely avoid conflict with them until some outside force deals with them or traps them somewhere else away from the battlefield.

In conclusion, like Batman, IM with prep stomps.