The ruins of the palace have been found in the Kaidecho neighbourhood of the city of Mukō and have been designated as a National Historic Site since 1964, with the area under protection expanded in 2016.

The imperial palace was situated on a minor plateau 15 meters higher than the city, visually demonstrating the authority of the emperor, whereas Heijō-kyō was completely flat.

Nonetheless, in September of the same year, Fujiwara no Tanetsugu was assassinated, and several officials associated with the great state temple of Tōdai-ji were implicated.

Emperor Kanmu's younger brother, Imperial Prince Sawara, was also imprisoned and exiled because of his strong opposition to the move of the capital.

Despite efforts at appeasing the prince's spirit, heavy rains followed by floods caused great damage to Nagaoka-kyō.

[2] After the transfer of the capital, the former Nagaoka-kyō area became the domain of Sugawara no Michizane, and the Nagaoka Tenman-gu Shinto shrine was constructed after his exile in 901.