On 15 May 1944, "Nagara" replaced the cruiser as flagship of 11th Destroyer Flotilla, directly under the Combined Fleet. She remained in Japanese home waters training with new destroyers and escorting a convoy to the Ogasawara Islands in June and to Okinawa in July. In another refit at Yokosuka Naval Arsenal on 2 July 1944, ten single-mount Type 96 25-mm AA guns were installed, bringing "Nagara"s 25-mm total to 32 barrels (2X3, 6x2, 14x1). A Type 22 surface-search radar was fitted.