Nagasaki had a strange structure. Ōmura Sumitada gave the Jesuits the rights to administer Nagasaki and Mogi (Nagasaki's port village at the time). Sumitada himself actually retained the right to levy customs duties, which came to over 1000 silver coins a year, and he was also the Jesuit's nominal overlord. Sumitada was also the nominal lord to judges that oversaw the courts that ruled the Japanese population. In practice though, the Jesuits were the ones to appoint said judges, and the Jesuits also oversaw the application of canonical law. Civil law for the Portuguese population were maintained under the authority of the Captain Major. So Nagasaki was neither a pure Portuguese colony nor a pure Sumitada's domain, but a bit of both.

It's pretty clear the Jesuits made if not every then at least the important decisions of the city. Besides setting down the law the Jesuits also immediately went about fortifying Nagasaki and Mogi, setting aside 150 silver coins out of 700 they receive from anchorage dues to build the defenses with ramparts, moats, bastions, and cannons. The city itself seem to have been designed based on Lisbon, which was quite geographically similar (perhaps a reason the site was chosen), though the city's layout kept the East-Asian grid pattern. The Jesuits also ordered the construction of what was probably the first European-style warship (or ships, it's unclear) made in Japan, which would play an important role that lead to Hideyoshi's order for the expulsion of Jesuits and for them to give up Nagasaki in 1587. For the ship's captain they picked one Ambrosio Fernandes, a soldier-turned-merchant who had promised to God he'd join the Jesuits Society if God saved him from a storm he ran into. For our purposes it tells us the Jesuits were also the ones making the military personnel decisions, at least the important ones. Though given that they had a huge (by Japanese standards) ship and a captain with some merchant backgrounds, the ship likely also conducted some local trade and brought supplies to and from Nagasaki, while it's patrolling the nearby waters and fighting local wars. This the Jesuits did a plenty to expand their influences and help Christian lords.

By 1584-85, the Shimazu had actually expanded their influence into the area and they demanded the Jesuit's submission in person with each padre to bring a spear. The Jesuits instead sent the leading citizens of Nagasaki on the excuse the Jesuits were not soldiers (not sure if anyone would've believed them) and expensive gifts and their word of submission. From this we can see that the Jesuits again was very much in charge of the other people of the city as well as its diplomacy, if the latter wasn't clear enough already. However, even by 1585 they could not travel to Kyōto without the Shimazu's permission. They were very much power of Kyūshū political, military, and diplomatic structure whether they wanted it, to spread Christianity, or not, when the leading Jesuit of Nagasaki at the time, Gasper Coeho, had to wait for a new year when he hoped the Shimazu would be too busy with the Ōtomo to go after him to slip away to Kyōto. It turns out they weren't, but he got what he set out to get, and what the Shimzau had wished to prevent, Hideyoshi's help with the Shimazu.

Coelho admits in 1587, while trying the evade blame for it, that the Jesuits were actively involved in the slave trade of the area. This is despite the trade giving them a bad reputation in Japan, and despite the society itself having requested the King's orders, issued in 1570, to outlaw slave trading in Japan. Still, Jesuits priests issued the licenses and certificates for the slave trade. Coelho's excuse is that the Jesuit priests were fooled by evil merchants into believing that the slaves were obtained legally. Here we can see another aspect of daily life and the power structure in Nagasaki. The Jesuits were the rulers issuing trade licenses and certificates for goods, including slaves, for merchants who "donated to" and obeyed the Jesuit's request. The Jesuit's compound was compared to the customs house of Seville, showing us the amount of goods, again including slaves, that pass through their hands. By this time, within less than 20 years, the profits from one annual trade mission had doubled to 200,000 silver coins a year. Goods from China would be loaded up in Macau, shipped to Nagasaki (or sometimes Hirado) to be sold, and Japanese goods with slaves being especially cheap to buy due to famine in Kyūshū at the time, being packed onto the Carrack(s) and shipped out.

In his edict for the expulsion of the Jesuits, Hideyoshi compared them to the Ikkō-ikki. When considering the way the Jesuits ruled Nagasaki and influenced local politics and wars, the comparison is actually fairly spot on.