You're probably well aware of ninjas, but ninjas were used on several occasions as a raid force by Tokugawa Ieyasu. For instance, during the Christian Shimabara rebellion, they infiltrated the castle on several occasions and stole food supplies, as well as gathered intelligence on the defenders.

To be more specific, Ninja at the time were typically raised in Kaga domain, in the north of the Kansai region of Japan, and Iga domain, located in the southern part of Kansai. . When Tokugawa Ieyasu came to power in the later 1500s/early 1600s, he retained a large group of ninja (one of the most famous ones being Hattori Hanzo, who has been the subject of many a Japanese historical fiction).

While they often served as bodyguards (for instance, Hanzo escorted Tokugawa to safety after the chaos of Oda Nobunaga's assassination), they were also tasked with special operations. A popular use of them was in preparation for night combat. As they were typically camouflaged and highly mobile, they were able to infiltrate into forts, whereupon they would attack the defenders from the inside and set the installations on fire-Tokugawa used some ninja from Koga in a raid on an Imagawa fort. Similarly, Fuma Kotaro, the head of a group of ninja/brigands, launched a surprise attack on one of Takeda Katsuyori's camps at night, causing confusion in the camp, and quite a bit of friendly fire.

Then you had ninja used for espionage. Probably one of the best was Mochizuki Chiyome, a noblewoman under Takeda Shingen. Takeda asked her to help him create an espionage network throughout Japan to gather information. She proceeded to find women-orphans, widows, and such-and trained them to be spies, including disguises that would allow them to travel (such as miko, the Shinto shrine maidens).

This took place in the 1500s-1600s, so it may be somewhat out of the time period that you are looking for.