Generally, Naomasa has a good relationship with her younger sister, but often their different personalities cause friction between them. He is very much adheres to follow the laws and proper procedures, while Makoto is more rebellious and much more predisposed to challenge the rules and authority.
It does not help that Makoto knows the Naruhata Vigilantes personally, whom Naomasa does not consider much better than the criminals, or the fact that she often asks him about any villains or hero information he has learned of, to which he replies that he cannot leak any confidential information.
Despite this, Naomasa cares for her, and often warns her not to approach into any danger.
Naomasa is a good friend of All Might and one of the few people that knows about the hero's condition and his true identity as Tosinori Yagi, though he only found that out as a complete accident. However, he promised to keep the secret, and since then they have remained good friends, with Naomasa being one of the few individuals that Toshinori fully trusts and can confide with.
Professionally the two also have a special relationship. Naomasa is a vital ally of All Might, supplying him with information about investigations on matters related to the the League of Villains and the All For One. Naomasa is also the one taking care of the paperwork for All Might unauthorized random hero acts to make sure All Might is kept on the up and up.
All Might thinks he is the best cop there is, which shows how much faith he has in him.
As one of the few people who knows the secret of All Might, Naomasa usually collaborates with Gran Torino, especially after All Might loses the One For All and stop being a hero, Naomasa and Gran Torino work together in the investigations on the activities of the League of Villains, and thus be able to find and arrest all its members.