In 1558, Rokkaku Yoshikata employed a team of ninja to set fire to Sawayama Castle. A chūnin captain led a force of 48 ninja into the castle by means of deception. In a technique dubbed bakemono-jutsu ("ghost technique"), his men stole a lantern bearing the enemy's family crest (mon), and proceeded to make replicas with the same mon. By wielding these lanterns, they were allowed to enter the castle without a fight. Once inside, the ninja set fire to the castle, and Yoshitaka's army would later emerge victorious. The mercenary nature of the shinobi is demonstrated in another arson attack soon after the burning of Sawayama Castle. In 1561, commanders acting under Kizawa Nagamasa hired three Iga ninja of genin rank to assist the conquest of a fortress in Maibara. Rokkaku Yoshitaka, the same man who had hired Iga ninja just years earlier, was the fortress holder—and target of attack. The Asai Sandaiki writes of their plans: "We employed shinobi-no-mono of Iga... They were contracted to set fire to the castle". However, the mercenary shinobi were unwilling to take commands. When the fire attack did not begin as scheduled, the Iga men told the commanders, who were not from the region, that they could not possibly understand the tactics of the shinobi. They then threatened to abandon the operation if they were not allowed to act on their own strategy. The fire was eventually set, allowing Nagamasa's army to capture the fortress in a chaotic rush.
Following the Battle of Okehazama in 1560, Tokugawa employed a group of eighty Kōga ninja, led by Tomo Sukesada. They were tasked to raid an outpost of the Imagawa clan. The account of this assault is given in the Mikawa Go Fudoki, where it was written that Kōga ninja infiltrated the castle, set fire to its towers, and killed the castellan along with two hundred of the garrison. The Kōga ninja are said to have played a role in the later Battle of Sekigahara (1600), where several hundred Kōga assisted soldiers under Torii Mototada in the defence of Fushimi Castle. After Tokugawa's victory at Sekigahara, the Iga acted as guards for the inner compounds of Edo Castle, while the Kōga acted as a police force and assisted in guarding the outer gate. In 1614, the initial "winter campaign" at the Siege of Osaka saw the ninja in use once again. Miura Yoemon, a ninja in Tokugawa's service, recruited shinobi from the Iga region, and sent 10 ninja into Osaka Castle in an effort to foster antagonism between enemy commanders. During the later "summer campaign", these hired ninja fought alongside regular troops at the Battle of Tennōji.
The warlord Oda Nobunaga's notorious reputation led to several attempts on his life. In 1571, a Kōga ninja and sharpshooter by the name of Sugitani Zenjubō was hired to assassinate Nobunaga. Using two arquebuses, he fired two consecutive shots at Nobunaga, but was unable to inflict mortal injury through Nobunaga's armor. Sugitani managed to escape, but was caught four years later and put to death by torture. In 1573, Manabe Rokurō, a vassal of daimyō Hatano Hideharu, attempted to infiltrate Azuchi Castle and assassinate the sleeping Nobunaga. However, this also ended in failure, and Manabe was forced to commit suicide, after which his body was openly displayed in public. According to a document, the Iranki, when Nobunaga was inspecting Iga province—which his army had devastated—a group of three ninja shot at him with large-caliber firearms. The shots flew wide of Nobunaga, however, and instead killed seven of his surrounding companions.
A distinction is to be made between the ninja from these areas, and commoners or samurai hired as spies or mercenaries. Unlike their counterparts, the Iga and Kōga clans were professionals, specifically trained for their roles. These professional ninja were actively hired by daimyōs between 1485 and 1581. Specifically, the Iga professionals were sought after for their skill at siege warfare, or "shirotori", which included night attacks and ambush. By the 1460s, the leading families in the regions had established de facto independence from their shugo. The Kōka ikki persisted until 1574, when it was forced to become a vassal of Oda Nobunaga. The Iga ikki continued until 1581, when Nobunaga invaded Iga Province and wiped out the organized clans. Survivors were forced to flee, some to the mountains of Kii, but others arrived before Tokugawa Ieyasu, where they were well treated. Some former Iga clan members, including Hattori Hanzō, would later serve as Tokugawa's bodyguards. Prior to the conquest of Kōka in 1574, the two confederacies worked in alliance together from at least 1487.
On June 19, 2022, Kōka city in Shiga Prefecture announced that a written copy of "Kanrinseiyo", which is the original source of a famous book on the art of ninja called "Bansenshukai" (1676) from the Edo period was discovered in a warehouse of Kazuraki Shrine. The handwritten reproduction was produced in 1748. The book describes 48 types of ninjutsu. It has information about specific methods such as attaching layers of cotton to the bottom of straw sandals to prevent noise when sneaking around, attacking to the right when surrounded by a large number of enemies, throwing charred owl and turtle powder when trying to hide, and casting spells. It also clarified methods and how to manufacture and use ninjutsu tools, such as cane swords and "makibishi" (Japanese caltrop).
Although shorter swords and daggers were used, the katana was probably the ninja's weapon of choice, and was sometimes carried on the back. The katana had several uses beyond normal combat. In dark places, the scabbard could be extended out of the sword, and used as a long probing device. The sword could also be laid against the wall, where the ninja could use the sword guard (tsuba) to gain a higher foothold. The katana could even be used as a device to stun enemies before attacking them, by putting a combination of red pepper, dirt or dust, and iron filings into the area near the top of the scabbard, so that as the sword was drawn the concoction would fly into the enemy's eyes, stunning him until a lethal blow could be made. While straight swords were used before the invention of the katana, there's no known historical information about the straight ninjatō pre-20th century. The first photograph of a ninjatō appeared in a booklet by Heishichirō Okuse in 1956. A replica of a ninjatō is on display at the Ninja Museum of Igaryu.
In 2012, Jinichi Kawakami, the last authentic heir of ninjutsu, decided against passing on his teaching to any student, stating that the art of ninjutsu has no place in modern times. Instead, Kawakami serves as the honorary director of the Iga-ryu Ninja Museum and researches ninjutsu as a specially appointed professor at Mie University.
Mie University founded the world's first research centre devoted to the ninja in 2017. A graduate master course opened in 2018. It is located in Iga (now Mie Prefecture). There are approximately 3 student enrollments per year. Students must pass an admission test about Japanese history and be able to read historical ninja documents. Scientific researchers and scholars of different disciplines study ancient documents and how it can be used in the modern world.
On February 25, 2018, Yamada Yūji, the professor of Mie University and historian Nakanishi Gō announced that they had identified three people who were successful in early modern Ureshino, including the ninja Benkei Musō (弁慶夢想). Musō is thought to be the same person as Denrinbō Raikei (伝林坊頼慶), the Chinese disciple of Marume Nagayoshi, and possibly a pseudonym.
In 2020, the 45-year-old Genichi Mitsuhashi was the first student to graduate from the master course of ninja studies at Mie University. For 2 years he studied historical records and the traditions of the martial art. Similar to the original ninja, by day he was a farmer and grew vegetables while he did ninja studies and trained martial arts in the afternoon.