This pagoda (Skt. stūpa) rests on a two-level podium. It is a type known as a “Jeweled Pagoda,” and it likely would have been placed at the center of the square altar for rites of Esoteric Buddhism (J. mikkyō). A container enshrining relics of the Buddha is thought to have been placed inside its cylindrical body enclosed by a balustrade. The doors open to reveal colorful paintings of the Heavenly Guardians of the Eight Directions on each face. 
Object label 

Buddhist relics were enshrined in this small-scale pagoda, which would have been placed on the altar for rites of esoteric Buddhism (mikkyō). The inner surfaces of its doors feature the eight mikkyō deities who serve as the guardians of the eight directions. The two-tiered base for the pagoda is adorned with lotus flowers and lions. Pagodas of this shape with a single-storied cylindrical body were used in mikkyō contexts.
 
NAITO SakaeEnglish by Mary Lewine 
Buddhist Art Paradise: Jewels of the Nara National Museum. Nara National Museum, 2021.7, p.341, no.111. 

This is a hōtō-type stupa of reduced size. It is conceivable that it had been used as a relic container by keeping a relic case within the stupa.
The stupa-body has a roof with the depiction of roof tiles and a sōrin-spire with a flaming magic jewel attached to the top of the roof. The cylindrical interior space is surrounded by a corridor and a railing. Double-doors are located at the four sides of the interior space. The inside of each door-panel is decorated with a painting of eight guardian deities in colors and gold foil. Staircases are modeled at the four sides of the base-part of the stupa. Kōzama openwork decorations are in the baseboards.
Other well known wooden miniature stupas are the five-storied stupa in Tō-ji temple made in 1240, the tahō-tō-type stupa of Sankeien in Kanagawa prefecture made in 1450, a stupa in Jūrin-in temple in Nara, and others. There are some extant examples which were made during and after the middle ages. The miniature stupa introduced in this article is a notable example of the small wooden stupa category. 
Masterpieces of Nara National Museum. Nara National Museum, 1993, p.107, no.83.